Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.py @ 52:ae12977c0e5e draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
author fubar
date Thu, 07 Mar 2024 06:41:01 +0000
parents 460d5b6c5d98
children bdfa6a7c4543
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1 import argparse
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2 import logging
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3 import os
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4 import sys
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5
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6 from jbrowse2 import JbrowseConnector as jbC
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8 logging.basicConfig(level=logging.debug)
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9 log = logging.getLogger("jbrowse")
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11
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12 def makeDefaultLocation():
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13
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14 refName = jc.genome_firstcontig
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15 defloc = "%s:100..10000" % refName
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16 return defloc
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19 if __name__ == "__main__":
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20 parser = argparse.ArgumentParser(description="", epilog="")
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21 parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
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22 parser.add_argument(
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23 "--trackmeta",
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24 help="Repeatable 'filename,filext,filepath,[bai/crai path for filesystem bam/cram]' for JBrowse2 tracks",
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25 default=[],
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26 action="append",
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27 )
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28 parser.add_argument(
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29 "--referencemeta",
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30 help="Repeatable 'filename, filext, filepath, ... ,' for JBrowse2 reference tracks - usually only one needed",
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31 default=[],
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32 action="append",
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33 )
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34 parser.add_argument(
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35 "--pafmeta",
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36 help="Repeatable. Each is a 'pafname, filext, filepath, ... ,' for a JBrowse2 paf track",
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37 default=[],
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38 action="append",
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39 )
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40 parser.add_argument(
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41 "--pafreferencemeta",
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42 help="Repeatable. Each is a 'pafname,refpath,refname' Every pafname must have one or more",
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43 default=[],
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44 action="append",
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45 )
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46 parser.add_argument(
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47 "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
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48 )
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49 parser.add_argument("--outdir", help="Output directory", required=True)
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50 parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.10.2")
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51 args = parser.parse_args()
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52 sessName = args.sessName
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53 # --trackmeta $jbrowseme[$key],$jbrowseme[$key].ext,'$key'
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54 trackList = [x.strip().split(",") for x in args.trackmeta if x > ""]
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55 refList = [x.strip().split(",") for x in args.referencemeta if x > ""]
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56 if len(refList) > 0:
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57 listgenomes = [f for f in refList if f[1] in ["fasta", "fasta.gz"]]
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58 # assume no pafs here
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59 if len(listgenomes) > 0:
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60 genome_paths = [x[0] for x in listgenomes]
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61 genome_names = [x[2] for x in listgenomes]
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62 guseuri = []
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63 for x in genome_paths:
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64 if x.startswith('http://') or x.startswith('https://'):
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65 guseuri.append('yes')
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66 else:
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67 guseuri.append('no')
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68 jc = jbC(
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69 outdir=args.outdir,
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70 jbrowse2path=args.jbrowse2path,
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71 genomes=[
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72 {
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73 "path": x,
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74 "label": genome_names[i],
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75 "useuri": guseuri[i],
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76 "meta": {"name": genome_names[i],
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77 "dataset_dname": genome_names[i]
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78 }
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79 }
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80 for i, x in enumerate(genome_paths)
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81 ],
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82 )
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83
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84 jc.process_genomes()
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85 default_session_data = {
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86 "visibility": {
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87 "default_on": [],
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88 "default_off": [],
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89 },
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90 "style": {},
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91 "style_labels": {},
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92 }
35
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93 listtracks = trackList
30
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94 # foo.paf must have a foo_paf.fasta or fasta.gz to match
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95 tnames = [x[2] for x in listtracks]
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96 texts = [x[1] for x in listtracks]
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97 for i, track in enumerate(listtracks):
52
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98 track_conf = {"trackfiles": [], "category": "autogenerated"}
35
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99 tpath, trext, trackname = track[:3]
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100 track_conf["dataset_id"] = trackname
52
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101 useuri = "no"
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102 if tpath.startswith('http://') or tpath.startswith('https://'):
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103 useuri = "yes"
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104 if trext == "paf":
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105 refname = trackname + "_paf.fasta"
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106 refdat = [x[2] for x in listtracks if x[2] == refname]
30
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107 if not refdat:
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108 jc.logging.warn(
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109 "!! No reference file %s corresponding to paf file %s found. Not building - there must be a corresponding fasta for each paf"
35
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110 % (refname, trackname)
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111 )
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112 sys.exit(3)
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113 else:
48
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114 track_conf.update({
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115 "conf": {
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116 "options": {
35
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117 "paf": {"genome": refdat, "genome_label": trackname}
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118 }
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119 }
48
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120 })
46
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121 elif trext == "bam":
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122 ipath = track[3]
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123 if not os.path.exists(ipath):
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124 ipath = os.path.realpath(os.path.join(jc.outdir, trackname + '.bai'))
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125 cmd = ["samtools", "index", "-b", "-o", ipath, os.path.realpath(track[0])]
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126 sys.stdout.write('#### calling %s' % ' '.join(cmd))
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127 jc.subprocess_check_call(cmd)
48
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128 track_conf.update({"conf": {"options": {"bam": {"bam_index": ipath}}}})
46
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129 elif trext == "cram":
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130 ipath = track[3]
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131 if not os.path.exists(ipath):
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132 jc.logging.info('calling %s' % ' '.join(cmd))
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133 ipath = os.path.realpath(os.path.join('./', trackname + '.crai'))
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134 cmd = ["samtools", "index", "-c", "-o", ipath, os.path.realpath(track[0])]
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135 sys.stdout.write('#### calling %s' % ' '.join(cmd))
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136 jc.subprocess_check_call(cmd)
48
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137 track_conf.update({"conf": {"options": {"cram": {"cram_index": ipath}}}})
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138 track_conf["path"] = tpath
35
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139 track_conf["format"] = trext
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140 track_conf["name"] = trackname
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141 track_conf["label"] = trackname
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142 track_conf["trackfiles"].append((tpath, trext, useuri, trackname, {}))
30
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143 keys = jc.process_annotations(track_conf)
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144
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145 if keys:
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146 for key in keys:
46
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147 if trext in [
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148 "bigwig",
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149 "gff3",
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150 "gff",
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151 "vcf",
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152 "maf",
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153 ]:
35
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154 default_session_data["visibility"]["default_on"].append(key)
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155 else:
46
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156 default_session_data["visibility"]["default_off"].append(
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157 key
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diff changeset
158 )
30
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159 # general_data = {
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160 # "analytics": root.find("metadata/general/analytics").text,
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161 # "primary_color": root.find("metadata/general/primary_color").text,
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162 # "secondary_color": root.find("metadata/general/secondary_color").text,
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163 # "tertiary_color": root.find("metadata/general/tertiary_color").text,
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164 # "quaternary_color": root.find("metadata/general/quaternary_color").text,
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165 # "font_size": root.find("metadata/general/font_size").text,
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166 # }
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167 # jc.add_general_configuration(general_data)
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168 trackconf = jc.config_json.get("tracks", None)
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169 if trackconf:
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170 jc.config_json["tracks"].update(jc.tracksToAdd)
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171 else:
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172 jc.config_json["tracks"] = jc.tracksToAdd
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173 jc.write_config()
35
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174 defLoc = makeDefaultLocation()
46
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175 default_session_data.update(
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176 {"defaultLocation": defLoc, "session_name": sessName}
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177 )
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178 track_conf.update(default_session_data)
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179 jc.add_default_session(default_session_data)
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180 # jc.text_index() not sure what broke here.
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181 else:
46
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182 sys.stderr.write(
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183 "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
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184 )