Job ID = 6529344 SRX = SRX193327 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:10 41009766 reads; of these: 41009766 (100.00%) were unpaired; of these: 1564537 (3.82%) aligned 0 times 25662617 (62.58%) aligned exactly 1 time 13782612 (33.61%) aligned >1 times 96.18% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 10540543 / 39445229 = 0.2672 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.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 @ Tue, 30 Jun 2020 02:18:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:45: 1000000 INFO @ Tue, 30 Jun 2020 02:18:52: 2000000 INFO @ Tue, 30 Jun 2020 02:18:58: 3000000 INFO @ Tue, 30 Jun 2020 02:19:05: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.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 @ Tue, 30 Jun 2020 02:19:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:11: 5000000 INFO @ Tue, 30 Jun 2020 02:19:15: 1000000 INFO @ Tue, 30 Jun 2020 02:19:18: 6000000 INFO @ Tue, 30 Jun 2020 02:19:22: 2000000 INFO @ Tue, 30 Jun 2020 02:19:25: 7000000 INFO @ Tue, 30 Jun 2020 02:19:28: 3000000 INFO @ Tue, 30 Jun 2020 02:19:31: 8000000 INFO @ Tue, 30 Jun 2020 02:19:35: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:19:38: 9000000 INFO @ Tue, 30 Jun 2020 02:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.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 @ Tue, 30 Jun 2020 02:19:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:42: 5000000 INFO @ Tue, 30 Jun 2020 02:19:45: 10000000 INFO @ Tue, 30 Jun 2020 02:19:46: 1000000 INFO @ Tue, 30 Jun 2020 02:19:48: 6000000 INFO @ Tue, 30 Jun 2020 02:19:52: 11000000 INFO @ Tue, 30 Jun 2020 02:19:53: 2000000 INFO @ Tue, 30 Jun 2020 02:19:55: 7000000 INFO @ Tue, 30 Jun 2020 02:19:59: 12000000 INFO @ Tue, 30 Jun 2020 02:19:59: 3000000 INFO @ Tue, 30 Jun 2020 02:20:02: 8000000 INFO @ Tue, 30 Jun 2020 02:20:06: 13000000 INFO @ Tue, 30 Jun 2020 02:20:06: 4000000 INFO @ Tue, 30 Jun 2020 02:20:09: 9000000 INFO @ Tue, 30 Jun 2020 02:20:13: 14000000 INFO @ Tue, 30 Jun 2020 02:20:13: 5000000 INFO @ Tue, 30 Jun 2020 02:20:15: 10000000 INFO @ Tue, 30 Jun 2020 02:20:19: 15000000 INFO @ Tue, 30 Jun 2020 02:20:20: 6000000 INFO @ Tue, 30 Jun 2020 02:20:22: 11000000 INFO @ Tue, 30 Jun 2020 02:20:26: 16000000 INFO @ Tue, 30 Jun 2020 02:20:27: 7000000 INFO @ Tue, 30 Jun 2020 02:20:29: 12000000 INFO @ Tue, 30 Jun 2020 02:20:33: 17000000 INFO @ Tue, 30 Jun 2020 02:20:34: 8000000 INFO @ Tue, 30 Jun 2020 02:20:36: 13000000 INFO @ Tue, 30 Jun 2020 02:20:39: 18000000 INFO @ Tue, 30 Jun 2020 02:20:41: 9000000 INFO @ Tue, 30 Jun 2020 02:20:43: 14000000 INFO @ Tue, 30 Jun 2020 02:20:46: 19000000 INFO @ Tue, 30 Jun 2020 02:20:48: 10000000 INFO @ Tue, 30 Jun 2020 02:20:50: 15000000 INFO @ Tue, 30 Jun 2020 02:20:52: 20000000 INFO @ Tue, 30 Jun 2020 02:20:55: 11000000 INFO @ Tue, 30 Jun 2020 02:20:56: 16000000 INFO @ Tue, 30 Jun 2020 02:20:59: 21000000 INFO @ Tue, 30 Jun 2020 02:21:02: 12000000 INFO @ Tue, 30 Jun 2020 02:21:03: 17000000 INFO @ Tue, 30 Jun 2020 02:21:05: 22000000 INFO @ Tue, 30 Jun 2020 02:21:08: 13000000 INFO @ Tue, 30 Jun 2020 02:21:10: 18000000 INFO @ Tue, 30 Jun 2020 02:21:11: 23000000 INFO @ Tue, 30 Jun 2020 02:21:15: 14000000 INFO @ Tue, 30 Jun 2020 02:21:17: 19000000 INFO @ Tue, 30 Jun 2020 02:21:18: 24000000 INFO @ Tue, 30 Jun 2020 02:21:22: 15000000 INFO @ Tue, 30 Jun 2020 02:21:23: 20000000 INFO @ Tue, 30 Jun 2020 02:21:24: 25000000 INFO @ Tue, 30 Jun 2020 02:21:29: 16000000 INFO @ Tue, 30 Jun 2020 02:21:30: 21000000 INFO @ Tue, 30 Jun 2020 02:21:31: 26000000 INFO @ Tue, 30 Jun 2020 02:21:35: 17000000 INFO @ Tue, 30 Jun 2020 02:21:37: 22000000 INFO @ Tue, 30 Jun 2020 02:21:37: 27000000 INFO @ Tue, 30 Jun 2020 02:21:42: 18000000 INFO @ Tue, 30 Jun 2020 02:21:43: 23000000 INFO @ Tue, 30 Jun 2020 02:21:44: 28000000 INFO @ Tue, 30 Jun 2020 02:21:49: 19000000 INFO @ Tue, 30 Jun 2020 02:21:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:50: #1 total tags in treatment: 28904686 INFO @ Tue, 30 Jun 2020 02:21:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:21:50: 24000000 INFO @ Tue, 30 Jun 2020 02:21:51: #1 tags after filtering in treatment: 28904649 INFO @ Tue, 30 Jun 2020 02:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:53: #2 number of paired peaks: 783 WARNING @ Tue, 30 Jun 2020 02:21:53: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:53: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:21:53: #2 alternative fragment length(s) may be 1,25,42,598 bps INFO @ Tue, 30 Jun 2020 02:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.05_model.r WARNING @ Tue, 30 Jun 2020 02:21:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:53: #2 You may need to consider one of the other alternative d(s): 1,25,42,598 WARNING @ Tue, 30 Jun 2020 02:21:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:21:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:55: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:21:57: 25000000 INFO @ Tue, 30 Jun 2020 02:22:02: 21000000 INFO @ Tue, 30 Jun 2020 02:22:03: 26000000 INFO @ Tue, 30 Jun 2020 02:22:08: 22000000 INFO @ Tue, 30 Jun 2020 02:22:10: 27000000 INFO @ Tue, 30 Jun 2020 02:22:15: 23000000 INFO @ Tue, 30 Jun 2020 02:22:16: 28000000 INFO @ Tue, 30 Jun 2020 02:22:22: 24000000 INFO @ Tue, 30 Jun 2020 02:22:22: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:22:22: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:22:22: #1 total tags in treatment: 28904686 INFO @ Tue, 30 Jun 2020 02:22:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:22:23: #1 tags after filtering in treatment: 28904649 INFO @ Tue, 30 Jun 2020 02:22:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:25: #2 number of paired peaks: 783 WARNING @ Tue, 30 Jun 2020 02:22:25: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:26: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:22:26: #2 alternative fragment length(s) may be 1,25,42,598 bps INFO @ Tue, 30 Jun 2020 02:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.10_model.r WARNING @ Tue, 30 Jun 2020 02:22:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:26: #2 You may need to consider one of the other alternative d(s): 1,25,42,598 WARNING @ Tue, 30 Jun 2020 02:22:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:22:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:22:29: 25000000 INFO @ Tue, 30 Jun 2020 02:22:35: 26000000 INFO @ Tue, 30 Jun 2020 02:22:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:42: 27000000 INFO @ Tue, 30 Jun 2020 02:22:48: 28000000 INFO @ Tue, 30 Jun 2020 02:22:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:22:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:22:55: #1 total tags in treatment: 28904686 INFO @ Tue, 30 Jun 2020 02:22:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:22:55: #1 tags after filtering in treatment: 28904649 INFO @ Tue, 30 Jun 2020 02:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:22:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:22:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:22:58: #2 number of paired peaks: 783 WARNING @ Tue, 30 Jun 2020 02:22:58: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Tue, 30 Jun 2020 02:22:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:22:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:22:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:22:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:22:58: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:22:58: #2 alternative fragment length(s) may be 1,25,42,598 bps INFO @ Tue, 30 Jun 2020 02:22:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.20_model.r WARNING @ Tue, 30 Jun 2020 02:22:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:22:58: #2 You may need to consider one of the other alternative d(s): 1,25,42,598 WARNING @ Tue, 30 Jun 2020 02:22:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:22:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:22:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.05_summits.bed INFO @ Tue, 30 Jun 2020 02:23:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:23:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.10_summits.bed INFO @ Tue, 30 Jun 2020 02:23:38: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:23:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193327/SRX193327.20_summits.bed INFO @ Tue, 30 Jun 2020 02:24:09: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling