Job ID = 6453479 SRX = SRX1167418 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:19:17 prefetch.2.10.7: 1) Downloading 'SRR2192442'... 2020-06-21T08:19:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:22:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:22:58 prefetch.2.10.7: 1) 'SRR2192442' was downloaded successfully Read 42058541 spots for SRR2192442/SRR2192442.sra Written 42058541 spots for SRR2192442/SRR2192442.sra 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: 00:00:00 Multiseed full-index search: 00:14:28 42058541 reads; of these: 42058541 (100.00%) were unpaired; of these: 1683116 (4.00%) aligned 0 times 15301599 (36.38%) aligned exactly 1 time 25073826 (59.62%) aligned >1 times 96.00% overall alignment rate Time searching: 00:14:28 Overall time: 00:14:28 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] 11704819 / 40375425 = 0.2899 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 @ Sun, 21 Jun 2020 17:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.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 @ Sun, 21 Jun 2020 17:49:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:07: 1000000 INFO @ Sun, 21 Jun 2020 17:49:13: 2000000 INFO @ Sun, 21 Jun 2020 17:49:18: 3000000 INFO @ Sun, 21 Jun 2020 17:49:23: 4000000 INFO @ Sun, 21 Jun 2020 17:49:28: 5000000 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 @ Sun, 21 Jun 2020 17:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.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 @ Sun, 21 Jun 2020 17:49:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:34: 6000000 INFO @ Sun, 21 Jun 2020 17:49:38: 1000000 INFO @ Sun, 21 Jun 2020 17:49:40: 7000000 INFO @ Sun, 21 Jun 2020 17:49:44: 2000000 INFO @ Sun, 21 Jun 2020 17:49:46: 8000000 INFO @ Sun, 21 Jun 2020 17:49:50: 3000000 INFO @ Sun, 21 Jun 2020 17:49:52: 9000000 INFO @ Sun, 21 Jun 2020 17:49:56: 4000000 INFO @ Sun, 21 Jun 2020 17:49:58: 10000000 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 @ Sun, 21 Jun 2020 17:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.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 @ Sun, 21 Jun 2020 17:50:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:02: 5000000 INFO @ Sun, 21 Jun 2020 17:50:04: 11000000 INFO @ Sun, 21 Jun 2020 17:50:08: 6000000 INFO @ Sun, 21 Jun 2020 17:50:08: 1000000 INFO @ Sun, 21 Jun 2020 17:50:10: 12000000 INFO @ Sun, 21 Jun 2020 17:50:14: 7000000 INFO @ Sun, 21 Jun 2020 17:50:15: 2000000 INFO @ Sun, 21 Jun 2020 17:50:16: 13000000 INFO @ Sun, 21 Jun 2020 17:50:20: 8000000 INFO @ Sun, 21 Jun 2020 17:50:21: 3000000 INFO @ Sun, 21 Jun 2020 17:50:22: 14000000 INFO @ Sun, 21 Jun 2020 17:50:26: 9000000 INFO @ Sun, 21 Jun 2020 17:50:27: 4000000 INFO @ Sun, 21 Jun 2020 17:50:28: 15000000 INFO @ Sun, 21 Jun 2020 17:50:32: 10000000 INFO @ Sun, 21 Jun 2020 17:50:33: 5000000 INFO @ Sun, 21 Jun 2020 17:50:34: 16000000 INFO @ Sun, 21 Jun 2020 17:50:39: 11000000 INFO @ Sun, 21 Jun 2020 17:50:39: 6000000 INFO @ Sun, 21 Jun 2020 17:50:41: 17000000 INFO @ Sun, 21 Jun 2020 17:50:45: 12000000 INFO @ Sun, 21 Jun 2020 17:50:45: 7000000 INFO @ Sun, 21 Jun 2020 17:50:47: 18000000 INFO @ Sun, 21 Jun 2020 17:50:51: 13000000 INFO @ Sun, 21 Jun 2020 17:50:52: 8000000 INFO @ Sun, 21 Jun 2020 17:50:53: 19000000 INFO @ Sun, 21 Jun 2020 17:50:57: 14000000 INFO @ Sun, 21 Jun 2020 17:50:58: 9000000 INFO @ Sun, 21 Jun 2020 17:50:59: 20000000 INFO @ Sun, 21 Jun 2020 17:51:03: 15000000 INFO @ Sun, 21 Jun 2020 17:51:04: 10000000 INFO @ Sun, 21 Jun 2020 17:51:05: 21000000 INFO @ Sun, 21 Jun 2020 17:51:09: 16000000 INFO @ Sun, 21 Jun 2020 17:51:10: 11000000 INFO @ Sun, 21 Jun 2020 17:51:11: 22000000 INFO @ Sun, 21 Jun 2020 17:51:15: 17000000 INFO @ Sun, 21 Jun 2020 17:51:16: 12000000 INFO @ Sun, 21 Jun 2020 17:51:17: 23000000 INFO @ Sun, 21 Jun 2020 17:51:21: 18000000 INFO @ Sun, 21 Jun 2020 17:51:22: 13000000 INFO @ Sun, 21 Jun 2020 17:51:23: 24000000 INFO @ Sun, 21 Jun 2020 17:51:27: 19000000 INFO @ Sun, 21 Jun 2020 17:51:29: 14000000 INFO @ Sun, 21 Jun 2020 17:51:29: 25000000 INFO @ Sun, 21 Jun 2020 17:51:33: 20000000 INFO @ Sun, 21 Jun 2020 17:51:35: 15000000 INFO @ Sun, 21 Jun 2020 17:51:35: 26000000 INFO @ Sun, 21 Jun 2020 17:51:39: 21000000 INFO @ Sun, 21 Jun 2020 17:51:41: 16000000 INFO @ Sun, 21 Jun 2020 17:51:42: 27000000 INFO @ Sun, 21 Jun 2020 17:51:45: 22000000 INFO @ Sun, 21 Jun 2020 17:51:47: 17000000 INFO @ Sun, 21 Jun 2020 17:51:48: 28000000 INFO @ Sun, 21 Jun 2020 17:51:51: 23000000 INFO @ Sun, 21 Jun 2020 17:51:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:51:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:51:52: #1 total tags in treatment: 28670606 INFO @ Sun, 21 Jun 2020 17:51:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:51:52: #1 tags after filtering in treatment: 28670606 INFO @ Sun, 21 Jun 2020 17:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:53: 18000000 INFO @ Sun, 21 Jun 2020 17:51:54: #2 number of paired peaks: 1575 INFO @ Sun, 21 Jun 2020 17:51:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:55: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:51:55: #2 alternative fragment length(s) may be 1,19 bps INFO @ Sun, 21 Jun 2020 17:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.05_model.r WARNING @ Sun, 21 Jun 2020 17:51:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:55: #2 You may need to consider one of the other alternative d(s): 1,19 WARNING @ Sun, 21 Jun 2020 17:51:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:51:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:51:58: 24000000 INFO @ Sun, 21 Jun 2020 17:51:59: 19000000 INFO @ Sun, 21 Jun 2020 17:52:04: 25000000 INFO @ Sun, 21 Jun 2020 17:52:06: 20000000 INFO @ Sun, 21 Jun 2020 17:52:10: 26000000 INFO @ Sun, 21 Jun 2020 17:52:13: 21000000 INFO @ Sun, 21 Jun 2020 17:52:16: 27000000 INFO @ Sun, 21 Jun 2020 17:52:19: 22000000 INFO @ Sun, 21 Jun 2020 17:52:22: 28000000 INFO @ Sun, 21 Jun 2020 17:52:26: 23000000 INFO @ Sun, 21 Jun 2020 17:52:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:26: #1 total tags in treatment: 28670606 INFO @ Sun, 21 Jun 2020 17:52:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:52:27: #1 tags after filtering in treatment: 28670606 INFO @ Sun, 21 Jun 2020 17:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:29: #2 number of paired peaks: 1575 INFO @ Sun, 21 Jun 2020 17:52:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:29: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:52:29: #2 alternative fragment length(s) may be 1,19 bps INFO @ Sun, 21 Jun 2020 17:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.10_model.r WARNING @ Sun, 21 Jun 2020 17:52:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:29: #2 You may need to consider one of the other alternative d(s): 1,19 WARNING @ Sun, 21 Jun 2020 17:52:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:52:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:31: 24000000 INFO @ Sun, 21 Jun 2020 17:52:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:37: 25000000 INFO @ Sun, 21 Jun 2020 17:52:43: 26000000 INFO @ Sun, 21 Jun 2020 17:52:49: 27000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:52:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:52: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:55: 28000000 INFO @ Sun, 21 Jun 2020 17:52:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:59: #1 total tags in treatment: 28670606 INFO @ Sun, 21 Jun 2020 17:52:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:52:59: #1 tags after filtering in treatment: 28670606 INFO @ Sun, 21 Jun 2020 17:52:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:01: #2 number of paired peaks: 1575 INFO @ Sun, 21 Jun 2020 17:53:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:02: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:53:02: #2 alternative fragment length(s) may be 1,19 bps INFO @ Sun, 21 Jun 2020 17:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:02: #2 You may need to consider one of the other alternative d(s): 1,19 WARNING @ Sun, 21 Jun 2020 17:53:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:53:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.10_summits.bed INFO @ Sun, 21 Jun 2020 17:53:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167418/SRX1167418.20_summits.bed INFO @ Sun, 21 Jun 2020 17:54:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling