Job ID = 6454314 SRX = SRX197585 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:59:04 prefetch.2.10.7: 1) Downloading 'SRR597013'... 2020-06-21T08:59:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:07:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:07:07 prefetch.2.10.7: 1) 'SRR597013' was downloaded successfully Read 42007865 spots for SRR597013/SRR597013.sra Written 42007865 spots for SRR597013/SRR597013.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: 00:12:14 42007865 reads; of these: 42007865 (100.00%) were unpaired; of these: 1621726 (3.86%) aligned 0 times 29125706 (69.33%) aligned exactly 1 time 11260433 (26.81%) aligned >1 times 96.14% overall alignment rate Time searching: 00:12:14 Overall time: 00:12:14 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 12 files... [bam_rmdupse_core] 6030248 / 40386139 = 0.1493 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 18:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.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 18:30:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:38: 1000000 INFO @ Sun, 21 Jun 2020 18:30:44: 2000000 INFO @ Sun, 21 Jun 2020 18:30:50: 3000000 INFO @ Sun, 21 Jun 2020 18:30:56: 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 18:31:01: 5000000 INFO @ Sun, 21 Jun 2020 18:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.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 18:31:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:07: 6000000 INFO @ Sun, 21 Jun 2020 18:31:09: 1000000 INFO @ Sun, 21 Jun 2020 18:31:13: 7000000 INFO @ Sun, 21 Jun 2020 18:31:15: 2000000 INFO @ Sun, 21 Jun 2020 18:31:19: 8000000 INFO @ Sun, 21 Jun 2020 18:31:21: 3000000 INFO @ Sun, 21 Jun 2020 18:31:25: 9000000 INFO @ Sun, 21 Jun 2020 18:31:26: 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 18:31:31: 10000000 INFO @ Sun, 21 Jun 2020 18:31:32: 5000000 INFO @ Sun, 21 Jun 2020 18:31:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.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 18:31:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:37: 11000000 INFO @ Sun, 21 Jun 2020 18:31:38: 6000000 INFO @ Sun, 21 Jun 2020 18:31:39: 1000000 INFO @ Sun, 21 Jun 2020 18:31:43: 12000000 INFO @ Sun, 21 Jun 2020 18:31:44: 7000000 INFO @ Sun, 21 Jun 2020 18:31:45: 2000000 INFO @ Sun, 21 Jun 2020 18:31:49: 13000000 INFO @ Sun, 21 Jun 2020 18:31:50: 8000000 INFO @ Sun, 21 Jun 2020 18:31:51: 3000000 INFO @ Sun, 21 Jun 2020 18:31:55: 14000000 INFO @ Sun, 21 Jun 2020 18:31:56: 9000000 INFO @ Sun, 21 Jun 2020 18:31:57: 4000000 INFO @ Sun, 21 Jun 2020 18:32:01: 15000000 INFO @ Sun, 21 Jun 2020 18:32:02: 10000000 INFO @ Sun, 21 Jun 2020 18:32:03: 5000000 INFO @ Sun, 21 Jun 2020 18:32:07: 16000000 INFO @ Sun, 21 Jun 2020 18:32:08: 11000000 INFO @ Sun, 21 Jun 2020 18:32:09: 6000000 INFO @ Sun, 21 Jun 2020 18:32:14: 17000000 INFO @ Sun, 21 Jun 2020 18:32:14: 12000000 INFO @ Sun, 21 Jun 2020 18:32:15: 7000000 INFO @ Sun, 21 Jun 2020 18:32:20: 18000000 INFO @ Sun, 21 Jun 2020 18:32:20: 13000000 INFO @ Sun, 21 Jun 2020 18:32:22: 8000000 INFO @ Sun, 21 Jun 2020 18:32:26: 14000000 INFO @ Sun, 21 Jun 2020 18:32:26: 19000000 INFO @ Sun, 21 Jun 2020 18:32:28: 9000000 INFO @ Sun, 21 Jun 2020 18:32:32: 15000000 INFO @ Sun, 21 Jun 2020 18:32:32: 20000000 INFO @ Sun, 21 Jun 2020 18:32:34: 10000000 INFO @ Sun, 21 Jun 2020 18:32:38: 16000000 INFO @ Sun, 21 Jun 2020 18:32:39: 21000000 INFO @ Sun, 21 Jun 2020 18:32:40: 11000000 INFO @ Sun, 21 Jun 2020 18:32:44: 17000000 INFO @ Sun, 21 Jun 2020 18:32:45: 22000000 INFO @ Sun, 21 Jun 2020 18:32:47: 12000000 INFO @ Sun, 21 Jun 2020 18:32:51: 18000000 INFO @ Sun, 21 Jun 2020 18:32:51: 23000000 INFO @ Sun, 21 Jun 2020 18:32:53: 13000000 INFO @ Sun, 21 Jun 2020 18:32:57: 19000000 INFO @ Sun, 21 Jun 2020 18:32:58: 24000000 INFO @ Sun, 21 Jun 2020 18:33:00: 14000000 INFO @ Sun, 21 Jun 2020 18:33:03: 20000000 INFO @ Sun, 21 Jun 2020 18:33:04: 25000000 INFO @ Sun, 21 Jun 2020 18:33:06: 15000000 INFO @ Sun, 21 Jun 2020 18:33:09: 21000000 INFO @ Sun, 21 Jun 2020 18:33:10: 26000000 INFO @ Sun, 21 Jun 2020 18:33:13: 16000000 INFO @ Sun, 21 Jun 2020 18:33:15: 22000000 INFO @ Sun, 21 Jun 2020 18:33:17: 27000000 INFO @ Sun, 21 Jun 2020 18:33:19: 17000000 INFO @ Sun, 21 Jun 2020 18:33:21: 23000000 INFO @ Sun, 21 Jun 2020 18:33:24: 28000000 INFO @ Sun, 21 Jun 2020 18:33:26: 18000000 INFO @ Sun, 21 Jun 2020 18:33:27: 24000000 INFO @ Sun, 21 Jun 2020 18:33:31: 29000000 INFO @ Sun, 21 Jun 2020 18:33:32: 19000000 INFO @ Sun, 21 Jun 2020 18:33:33: 25000000 INFO @ Sun, 21 Jun 2020 18:33:37: 30000000 INFO @ Sun, 21 Jun 2020 18:33:39: 20000000 INFO @ Sun, 21 Jun 2020 18:33:39: 26000000 INFO @ Sun, 21 Jun 2020 18:33:43: 31000000 INFO @ Sun, 21 Jun 2020 18:33:45: 21000000 INFO @ Sun, 21 Jun 2020 18:33:46: 27000000 INFO @ Sun, 21 Jun 2020 18:33:50: 32000000 INFO @ Sun, 21 Jun 2020 18:33:51: 22000000 INFO @ Sun, 21 Jun 2020 18:33:53: 28000000 INFO @ Sun, 21 Jun 2020 18:33:56: 33000000 INFO @ Sun, 21 Jun 2020 18:33:57: 23000000 INFO @ Sun, 21 Jun 2020 18:33:59: 29000000 INFO @ Sun, 21 Jun 2020 18:34:03: 34000000 INFO @ Sun, 21 Jun 2020 18:34:03: 24000000 INFO @ Sun, 21 Jun 2020 18:34:05: 30000000 INFO @ Sun, 21 Jun 2020 18:34:05: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:34:05: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:34:05: #1 total tags in treatment: 34355891 INFO @ Sun, 21 Jun 2020 18:34:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:05: #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 18:34:06: #1 tags after filtering in treatment: 34355891 INFO @ Sun, 21 Jun 2020 18:34:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:08: #2 number of paired peaks: 170 WARNING @ Sun, 21 Jun 2020 18:34:08: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sun, 21 Jun 2020 18:34:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:08: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:34:08: #2 alternative fragment length(s) may be 1,31 bps INFO @ Sun, 21 Jun 2020 18:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.05_model.r WARNING @ Sun, 21 Jun 2020 18:34:08: #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 18:34:08: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Sun, 21 Jun 2020 18:34:08: #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 18:34:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:09: 25000000 INFO @ Sun, 21 Jun 2020 18:34:11: 31000000 INFO @ Sun, 21 Jun 2020 18:34:15: 26000000 INFO @ Sun, 21 Jun 2020 18:34:18: 32000000 INFO @ Sun, 21 Jun 2020 18:34:22: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:34:24: 33000000 INFO @ Sun, 21 Jun 2020 18:34:29: 28000000 INFO @ Sun, 21 Jun 2020 18:34:31: 34000000 INFO @ Sun, 21 Jun 2020 18:34:33: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:34:33: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:34:33: #1 total tags in treatment: 34355891 INFO @ Sun, 21 Jun 2020 18:34:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:33: #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 18:34:34: #1 tags after filtering in treatment: 34355891 INFO @ Sun, 21 Jun 2020 18:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:35: 29000000 INFO @ Sun, 21 Jun 2020 18:34:36: #2 number of paired peaks: 170 WARNING @ Sun, 21 Jun 2020 18:34:36: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sun, 21 Jun 2020 18:34:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:37: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:34:37: #2 alternative fragment length(s) may be 1,31 bps INFO @ Sun, 21 Jun 2020 18:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.10_model.r WARNING @ Sun, 21 Jun 2020 18:34:37: #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 18:34:37: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Sun, 21 Jun 2020 18:34:37: #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 18:34:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:41: 30000000 INFO @ Sun, 21 Jun 2020 18:34:48: 31000000 INFO @ Sun, 21 Jun 2020 18:34:54: 32000000 INFO @ Sun, 21 Jun 2020 18:35:00: 33000000 INFO @ Sun, 21 Jun 2020 18:35:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:06: 34000000 INFO @ Sun, 21 Jun 2020 18:35:08: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:35:08: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:35:08: #1 total tags in treatment: 34355891 INFO @ Sun, 21 Jun 2020 18:35:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:08: #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 18:35:09: #1 tags after filtering in treatment: 34355891 INFO @ Sun, 21 Jun 2020 18:35:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:11: #2 number of paired peaks: 170 WARNING @ Sun, 21 Jun 2020 18:35:11: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sun, 21 Jun 2020 18:35:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:12: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:35:12: #2 alternative fragment length(s) may be 1,31 bps INFO @ Sun, 21 Jun 2020 18:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.20_model.r WARNING @ Sun, 21 Jun 2020 18:35:12: #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 18:35:12: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Sun, 21 Jun 2020 18:35:12: #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 18:35:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:35:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:56: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197585/SRX197585.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:34: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling