Job ID = 6458979 SRX = SRX5827843 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:53:10 prefetch.2.10.7: 1) Downloading 'SRR9051594'... 2020-06-21T12:53:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:00:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:00:21 prefetch.2.10.7: 1) 'SRR9051594' was downloaded successfully 2020-06-21T13:00:21 prefetch.2.10.7: 'SRR9051594' has 0 unresolved dependencies Read 58591094 spots for SRR9051594/SRR9051594.sra Written 58591094 spots for SRR9051594/SRR9051594.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:42 58591094 reads; of these: 58591094 (100.00%) were unpaired; of these: 4976343 (8.49%) aligned 0 times 42749304 (72.96%) aligned exactly 1 time 10865447 (18.54%) aligned >1 times 91.51% overall alignment rate Time searching: 00:14:43 Overall time: 00:14:43 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 24 files... [bam_rmdupse_core] 20895403 / 53614751 = 0.3897 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 22:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.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 22:33:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:33:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:33:49: 1000000 INFO @ Sun, 21 Jun 2020 22:33:55: 2000000 INFO @ Sun, 21 Jun 2020 22:34:00: 3000000 INFO @ Sun, 21 Jun 2020 22:34:06: 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 @ Sun, 21 Jun 2020 22:34:12: 5000000 INFO @ Sun, 21 Jun 2020 22:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.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 22:34:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:18: 6000000 INFO @ Sun, 21 Jun 2020 22:34:19: 1000000 INFO @ Sun, 21 Jun 2020 22:34:24: 7000000 INFO @ Sun, 21 Jun 2020 22:34:25: 2000000 INFO @ Sun, 21 Jun 2020 22:34:30: 8000000 INFO @ Sun, 21 Jun 2020 22:34:31: 3000000 INFO @ Sun, 21 Jun 2020 22:34:36: 9000000 INFO @ Sun, 21 Jun 2020 22:34:38: 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 @ Sun, 21 Jun 2020 22:34:42: 10000000 INFO @ Sun, 21 Jun 2020 22:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.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 22:34:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:44: 5000000 INFO @ Sun, 21 Jun 2020 22:34:48: 11000000 INFO @ Sun, 21 Jun 2020 22:34:50: 1000000 INFO @ Sun, 21 Jun 2020 22:34:50: 6000000 INFO @ Sun, 21 Jun 2020 22:34:55: 12000000 INFO @ Sun, 21 Jun 2020 22:34:56: 2000000 INFO @ Sun, 21 Jun 2020 22:34:56: 7000000 INFO @ Sun, 21 Jun 2020 22:35:01: 13000000 INFO @ Sun, 21 Jun 2020 22:35:03: 8000000 INFO @ Sun, 21 Jun 2020 22:35:03: 3000000 INFO @ Sun, 21 Jun 2020 22:35:08: 14000000 INFO @ Sun, 21 Jun 2020 22:35:09: 9000000 INFO @ Sun, 21 Jun 2020 22:35:10: 4000000 INFO @ Sun, 21 Jun 2020 22:35:14: 15000000 INFO @ Sun, 21 Jun 2020 22:35:15: 10000000 INFO @ Sun, 21 Jun 2020 22:35:16: 5000000 INFO @ Sun, 21 Jun 2020 22:35:21: 16000000 INFO @ Sun, 21 Jun 2020 22:35:22: 11000000 INFO @ Sun, 21 Jun 2020 22:35:23: 6000000 INFO @ Sun, 21 Jun 2020 22:35:27: 17000000 INFO @ Sun, 21 Jun 2020 22:35:28: 12000000 INFO @ Sun, 21 Jun 2020 22:35:29: 7000000 INFO @ Sun, 21 Jun 2020 22:35:34: 18000000 INFO @ Sun, 21 Jun 2020 22:35:35: 13000000 INFO @ Sun, 21 Jun 2020 22:35:35: 8000000 INFO @ Sun, 21 Jun 2020 22:35:40: 19000000 INFO @ Sun, 21 Jun 2020 22:35:41: 14000000 INFO @ Sun, 21 Jun 2020 22:35:42: 9000000 INFO @ Sun, 21 Jun 2020 22:35:47: 20000000 INFO @ Sun, 21 Jun 2020 22:35:48: 15000000 INFO @ Sun, 21 Jun 2020 22:35:48: 10000000 INFO @ Sun, 21 Jun 2020 22:35:53: 21000000 INFO @ Sun, 21 Jun 2020 22:35:54: 16000000 INFO @ Sun, 21 Jun 2020 22:35:54: 11000000 INFO @ Sun, 21 Jun 2020 22:35:59: 22000000 INFO @ Sun, 21 Jun 2020 22:36:00: 17000000 INFO @ Sun, 21 Jun 2020 22:36:01: 12000000 INFO @ Sun, 21 Jun 2020 22:36:06: 23000000 INFO @ Sun, 21 Jun 2020 22:36:06: 18000000 INFO @ Sun, 21 Jun 2020 22:36:07: 13000000 INFO @ Sun, 21 Jun 2020 22:36:12: 24000000 INFO @ Sun, 21 Jun 2020 22:36:13: 19000000 INFO @ Sun, 21 Jun 2020 22:36:13: 14000000 INFO @ Sun, 21 Jun 2020 22:36:18: 25000000 INFO @ Sun, 21 Jun 2020 22:36:19: 20000000 INFO @ Sun, 21 Jun 2020 22:36:20: 15000000 INFO @ Sun, 21 Jun 2020 22:36:24: 26000000 INFO @ Sun, 21 Jun 2020 22:36:25: 21000000 INFO @ Sun, 21 Jun 2020 22:36:26: 16000000 INFO @ Sun, 21 Jun 2020 22:36:31: 27000000 INFO @ Sun, 21 Jun 2020 22:36:31: 22000000 INFO @ Sun, 21 Jun 2020 22:36:32: 17000000 INFO @ Sun, 21 Jun 2020 22:36:37: 28000000 INFO @ Sun, 21 Jun 2020 22:36:38: 23000000 INFO @ Sun, 21 Jun 2020 22:36:39: 18000000 INFO @ Sun, 21 Jun 2020 22:36:44: 29000000 INFO @ Sun, 21 Jun 2020 22:36:44: 24000000 INFO @ Sun, 21 Jun 2020 22:36:45: 19000000 INFO @ Sun, 21 Jun 2020 22:36:50: 25000000 INFO @ Sun, 21 Jun 2020 22:36:50: 30000000 INFO @ Sun, 21 Jun 2020 22:36:52: 20000000 INFO @ Sun, 21 Jun 2020 22:36:56: 26000000 INFO @ Sun, 21 Jun 2020 22:36:56: 31000000 INFO @ Sun, 21 Jun 2020 22:36:58: 21000000 INFO @ Sun, 21 Jun 2020 22:37:03: 32000000 INFO @ Sun, 21 Jun 2020 22:37:03: 27000000 INFO @ Sun, 21 Jun 2020 22:37:04: 22000000 INFO @ Sun, 21 Jun 2020 22:37:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:37:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:37:08: #1 total tags in treatment: 32719348 INFO @ Sun, 21 Jun 2020 22:37:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:08: #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 22:37:08: #1 tags after filtering in treatment: 32719347 INFO @ Sun, 21 Jun 2020 22:37:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:09: 28000000 INFO @ Sun, 21 Jun 2020 22:37:11: 23000000 INFO @ Sun, 21 Jun 2020 22:37:11: #2 number of paired peaks: 132 WARNING @ Sun, 21 Jun 2020 22:37:11: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 21 Jun 2020 22:37:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:11: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:37:11: #2 alternative fragment length(s) may be 2,10,45 bps INFO @ Sun, 21 Jun 2020 22:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.05_model.r WARNING @ Sun, 21 Jun 2020 22:37:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:11: #2 You may need to consider one of the other alternative d(s): 2,10,45 WARNING @ Sun, 21 Jun 2020 22:37:11: #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 22:37:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:15: 29000000 INFO @ Sun, 21 Jun 2020 22:37:17: 24000000 INFO @ Sun, 21 Jun 2020 22:37:21: 30000000 INFO @ Sun, 21 Jun 2020 22:37:23: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:37:27: 31000000 INFO @ Sun, 21 Jun 2020 22:37:29: 26000000 INFO @ Sun, 21 Jun 2020 22:37:34: 32000000 INFO @ Sun, 21 Jun 2020 22:37:35: 27000000 INFO @ Sun, 21 Jun 2020 22:37:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:37:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:37:38: #1 total tags in treatment: 32719348 INFO @ Sun, 21 Jun 2020 22:37:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:37:38: #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 22:37:39: #1 tags after filtering in treatment: 32719347 INFO @ Sun, 21 Jun 2020 22:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:37:39: #1 finished! INFO @ Sun, 21 Jun 2020 22:37:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:37:41: 28000000 INFO @ Sun, 21 Jun 2020 22:37:41: #2 number of paired peaks: 132 WARNING @ Sun, 21 Jun 2020 22:37:41: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 21 Jun 2020 22:37:41: start model_add_line... INFO @ Sun, 21 Jun 2020 22:37:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:37:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:37:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:37:42: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:37:42: #2 alternative fragment length(s) may be 2,10,45 bps INFO @ Sun, 21 Jun 2020 22:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.10_model.r WARNING @ Sun, 21 Jun 2020 22:37:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:37:42: #2 You may need to consider one of the other alternative d(s): 2,10,45 WARNING @ Sun, 21 Jun 2020 22:37:42: #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 22:37:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:37:47: 29000000 INFO @ Sun, 21 Jun 2020 22:37:53: 30000000 INFO @ Sun, 21 Jun 2020 22:37:58: 31000000 INFO @ Sun, 21 Jun 2020 22:38:04: 32000000 INFO @ Sun, 21 Jun 2020 22:38:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:38:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:38:08: #1 total tags in treatment: 32719348 INFO @ Sun, 21 Jun 2020 22:38:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:08: #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 22:38:09: #1 tags after filtering in treatment: 32719347 INFO @ Sun, 21 Jun 2020 22:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:09: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:12: #2 number of paired peaks: 132 WARNING @ Sun, 21 Jun 2020 22:38:12: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sun, 21 Jun 2020 22:38:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:38:12: #2 alternative fragment length(s) may be 2,10,45 bps INFO @ Sun, 21 Jun 2020 22:38:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.20_model.r WARNING @ Sun, 21 Jun 2020 22:38:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:12: #2 You may need to consider one of the other alternative d(s): 2,10,45 WARNING @ Sun, 21 Jun 2020 22:38:12: #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 22:38:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.05_summits.bed INFO @ Sun, 21 Jun 2020 22:38:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:38:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:39:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.10_summits.bed INFO @ Sun, 21 Jun 2020 22:39:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827843/SRX5827843.20_summits.bed INFO @ Sun, 21 Jun 2020 22:39:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling