Job ID = 14167266 SRX = SRX8688921 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5753890 spots for SRR12174379/SRR12174379.sra Written 5753890 spots for SRR12174379/SRR12174379.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167866 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:44 5753890 reads; of these: 5753890 (100.00%) were unpaired; of these: 316187 (5.50%) aligned 0 times 4166053 (72.40%) aligned exactly 1 time 1271650 (22.10%) aligned >1 times 94.50% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 269525 / 5437703 = 0.0496 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Dec 2021 11:29:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:29:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:29:09: 1000000 INFO @ Fri, 10 Dec 2021 11:29:14: 2000000 INFO @ Fri, 10 Dec 2021 11:29:20: 3000000 INFO @ Fri, 10 Dec 2021 11:29:25: 4000000 INFO @ Fri, 10 Dec 2021 11:29:30: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:29:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:29:31: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:29:31: #1 total tags in treatment: 5168178 INFO @ Fri, 10 Dec 2021 11:29:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:29:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:29:31: #1 tags after filtering in treatment: 5168178 INFO @ Fri, 10 Dec 2021 11:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:29:31: #1 finished! INFO @ Fri, 10 Dec 2021 11:29:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:29:32: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 11:29:32: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 10 Dec 2021 11:29:32: start model_add_line... INFO @ Fri, 10 Dec 2021 11:29:32: start X-correlation... INFO @ Fri, 10 Dec 2021 11:29:32: end of X-cor INFO @ Fri, 10 Dec 2021 11:29:32: #2 finished! INFO @ Fri, 10 Dec 2021 11:29:32: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Dec 2021 11:29:32: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Dec 2021 11:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.05_model.r WARNING @ Fri, 10 Dec 2021 11:29:32: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:29:32: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Fri, 10 Dec 2021 11:29:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:29:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Dec 2021 11:29:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:29:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:29:40: 1000000 INFO @ Fri, 10 Dec 2021 11:29:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:29:46: 2000000 INFO @ Fri, 10 Dec 2021 11:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.05_summits.bed INFO @ Fri, 10 Dec 2021 11:29:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2296 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:29:53: 3000000 INFO @ Fri, 10 Dec 2021 11:29:59: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:30:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 10 Dec 2021 11:30:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:30:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:30:06: 5000000 INFO @ Fri, 10 Dec 2021 11:30:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:30:07: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:30:07: #1 total tags in treatment: 5168178 INFO @ Fri, 10 Dec 2021 11:30:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:30:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:30:07: #1 tags after filtering in treatment: 5168178 INFO @ Fri, 10 Dec 2021 11:30:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:30:07: #1 finished! INFO @ Fri, 10 Dec 2021 11:30:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:30:07: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 11:30:07: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 10 Dec 2021 11:30:07: start model_add_line... INFO @ Fri, 10 Dec 2021 11:30:08: start X-correlation... INFO @ Fri, 10 Dec 2021 11:30:08: end of X-cor INFO @ Fri, 10 Dec 2021 11:30:08: #2 finished! INFO @ Fri, 10 Dec 2021 11:30:08: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Dec 2021 11:30:08: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Dec 2021 11:30:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.10_model.r WARNING @ Fri, 10 Dec 2021 11:30:08: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:30:08: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Fri, 10 Dec 2021 11:30:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:30:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:30:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:30:10: 1000000 INFO @ Fri, 10 Dec 2021 11:30:16: 2000000 INFO @ Fri, 10 Dec 2021 11:30:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:30:23: 3000000 INFO @ Fri, 10 Dec 2021 11:30:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:30:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:30:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.10_summits.bed INFO @ Fri, 10 Dec 2021 11:30:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (762 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:30:29: 4000000 INFO @ Fri, 10 Dec 2021 11:30:36: 5000000 INFO @ Fri, 10 Dec 2021 11:30:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:30:37: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:30:37: #1 total tags in treatment: 5168178 INFO @ Fri, 10 Dec 2021 11:30:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:30:37: #1 tags after filtering in treatment: 5168178 INFO @ Fri, 10 Dec 2021 11:30:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:30:37: #1 finished! INFO @ Fri, 10 Dec 2021 11:30:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:30:37: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 11:30:37: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 10 Dec 2021 11:30:37: start model_add_line... INFO @ Fri, 10 Dec 2021 11:30:37: start X-correlation... INFO @ Fri, 10 Dec 2021 11:30:37: end of X-cor INFO @ Fri, 10 Dec 2021 11:30:37: #2 finished! INFO @ Fri, 10 Dec 2021 11:30:37: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Dec 2021 11:30:37: #2 alternative fragment length(s) may be 76 bps INFO @ Fri, 10 Dec 2021 11:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.20_model.r WARNING @ Fri, 10 Dec 2021 11:30:37: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:30:37: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Fri, 10 Dec 2021 11:30:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:30:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:30:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:30:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:30:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688921/SRX8688921.20_summits.bed INFO @ Fri, 10 Dec 2021 11:30:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling