Job ID = 6458789 SRX = SRX5436062 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:59:46 prefetch.2.10.7: 1) Downloading 'SRR8637394'... 2020-06-21T12:59:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:03:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:03:08 prefetch.2.10.7: 1) 'SRR8637394' was downloaded successfully Read 41167914 spots for SRR8637394/SRR8637394.sra Written 41167914 spots for SRR8637394/SRR8637394.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: 00:11:14 41167914 reads; of these: 41167914 (100.00%) were unpaired; of these: 1942183 (4.72%) aligned 0 times 27639365 (67.14%) aligned exactly 1 time 11586366 (28.14%) aligned >1 times 95.28% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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 16 files... [bam_rmdupse_core] 7058874 / 39225731 = 0.1800 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 22:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.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 22:24:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:19: 1000000 INFO @ Sun, 21 Jun 2020 22:24:24: 2000000 INFO @ Sun, 21 Jun 2020 22:24:29: 3000000 INFO @ Sun, 21 Jun 2020 22:24:34: 4000000 INFO @ Sun, 21 Jun 2020 22:24:38: 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 22:24:43: 6000000 INFO @ Sun, 21 Jun 2020 22:24:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.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 22:24:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:24:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:24:48: 7000000 INFO @ Sun, 21 Jun 2020 22:24:50: 1000000 INFO @ Sun, 21 Jun 2020 22:24:53: 8000000 INFO @ Sun, 21 Jun 2020 22:24:55: 2000000 INFO @ Sun, 21 Jun 2020 22:24:58: 9000000 INFO @ Sun, 21 Jun 2020 22:25:00: 3000000 INFO @ Sun, 21 Jun 2020 22:25:03: 10000000 INFO @ Sun, 21 Jun 2020 22:25:05: 4000000 INFO @ Sun, 21 Jun 2020 22:25:08: 11000000 INFO @ Sun, 21 Jun 2020 22:25:10: 5000000 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 22:25:13: 12000000 INFO @ Sun, 21 Jun 2020 22:25:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.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 22:25:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:25:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:25:15: 6000000 INFO @ Sun, 21 Jun 2020 22:25:18: 13000000 INFO @ Sun, 21 Jun 2020 22:25:20: 1000000 INFO @ Sun, 21 Jun 2020 22:25:20: 7000000 INFO @ Sun, 21 Jun 2020 22:25:23: 14000000 INFO @ Sun, 21 Jun 2020 22:25:25: 2000000 INFO @ Sun, 21 Jun 2020 22:25:25: 8000000 INFO @ Sun, 21 Jun 2020 22:25:28: 15000000 INFO @ Sun, 21 Jun 2020 22:25:30: 3000000 INFO @ Sun, 21 Jun 2020 22:25:31: 9000000 INFO @ Sun, 21 Jun 2020 22:25:33: 16000000 INFO @ Sun, 21 Jun 2020 22:25:35: 4000000 INFO @ Sun, 21 Jun 2020 22:25:36: 10000000 INFO @ Sun, 21 Jun 2020 22:25:38: 17000000 INFO @ Sun, 21 Jun 2020 22:25:40: 5000000 INFO @ Sun, 21 Jun 2020 22:25:41: 11000000 INFO @ Sun, 21 Jun 2020 22:25:43: 18000000 INFO @ Sun, 21 Jun 2020 22:25:45: 6000000 INFO @ Sun, 21 Jun 2020 22:25:46: 12000000 INFO @ Sun, 21 Jun 2020 22:25:48: 19000000 INFO @ Sun, 21 Jun 2020 22:25:50: 7000000 INFO @ Sun, 21 Jun 2020 22:25:51: 13000000 INFO @ Sun, 21 Jun 2020 22:25:53: 20000000 INFO @ Sun, 21 Jun 2020 22:25:55: 8000000 INFO @ Sun, 21 Jun 2020 22:25:56: 14000000 INFO @ Sun, 21 Jun 2020 22:25:58: 21000000 INFO @ Sun, 21 Jun 2020 22:26:00: 9000000 INFO @ Sun, 21 Jun 2020 22:26:01: 15000000 INFO @ Sun, 21 Jun 2020 22:26:04: 22000000 INFO @ Sun, 21 Jun 2020 22:26:05: 10000000 INFO @ Sun, 21 Jun 2020 22:26:06: 16000000 INFO @ Sun, 21 Jun 2020 22:26:09: 23000000 INFO @ Sun, 21 Jun 2020 22:26:10: 11000000 INFO @ Sun, 21 Jun 2020 22:26:11: 17000000 INFO @ Sun, 21 Jun 2020 22:26:14: 24000000 INFO @ Sun, 21 Jun 2020 22:26:15: 12000000 INFO @ Sun, 21 Jun 2020 22:26:15: 18000000 INFO @ Sun, 21 Jun 2020 22:26:19: 25000000 INFO @ Sun, 21 Jun 2020 22:26:21: 13000000 INFO @ Sun, 21 Jun 2020 22:26:21: 19000000 INFO @ Sun, 21 Jun 2020 22:26:24: 26000000 INFO @ Sun, 21 Jun 2020 22:26:26: 14000000 INFO @ Sun, 21 Jun 2020 22:26:26: 20000000 INFO @ Sun, 21 Jun 2020 22:26:29: 27000000 INFO @ Sun, 21 Jun 2020 22:26:31: 15000000 INFO @ Sun, 21 Jun 2020 22:26:31: 21000000 INFO @ Sun, 21 Jun 2020 22:26:34: 28000000 INFO @ Sun, 21 Jun 2020 22:26:36: 16000000 INFO @ Sun, 21 Jun 2020 22:26:37: 22000000 INFO @ Sun, 21 Jun 2020 22:26:39: 29000000 INFO @ Sun, 21 Jun 2020 22:26:41: 17000000 INFO @ Sun, 21 Jun 2020 22:26:42: 23000000 INFO @ Sun, 21 Jun 2020 22:26:44: 30000000 INFO @ Sun, 21 Jun 2020 22:26:46: 18000000 INFO @ Sun, 21 Jun 2020 22:26:47: 24000000 INFO @ Sun, 21 Jun 2020 22:26:49: 31000000 INFO @ Sun, 21 Jun 2020 22:26:51: 19000000 INFO @ Sun, 21 Jun 2020 22:26:52: 25000000 INFO @ Sun, 21 Jun 2020 22:26:55: 32000000 INFO @ Sun, 21 Jun 2020 22:26:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:26:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:26:56: #1 total tags in treatment: 32166857 INFO @ Sun, 21 Jun 2020 22:26:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:56: #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 22:26:56: 20000000 INFO @ Sun, 21 Jun 2020 22:26:56: #1 tags after filtering in treatment: 32166812 INFO @ Sun, 21 Jun 2020 22:26:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:58: 26000000 INFO @ Sun, 21 Jun 2020 22:26:58: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 22:26:58: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 22:26:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:59: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:26:59: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 21 Jun 2020 22:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.05_model.r WARNING @ Sun, 21 Jun 2020 22:26:59: #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 22:26:59: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 21 Jun 2020 22:26:59: #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 22:26:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:27:01: 21000000 INFO @ Sun, 21 Jun 2020 22:27:03: 27000000 INFO @ Sun, 21 Jun 2020 22:27:07: 22000000 INFO @ Sun, 21 Jun 2020 22:27:09: 28000000 INFO @ Sun, 21 Jun 2020 22:27:12: 23000000 INFO @ Sun, 21 Jun 2020 22:27:14: 29000000 INFO @ Sun, 21 Jun 2020 22:27:17: 24000000 INFO @ Sun, 21 Jun 2020 22:27:19: 30000000 INFO @ Sun, 21 Jun 2020 22:27:22: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:27:24: 31000000 INFO @ Sun, 21 Jun 2020 22:27:27: 26000000 INFO @ Sun, 21 Jun 2020 22:27:29: 32000000 INFO @ Sun, 21 Jun 2020 22:27:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:27:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:27:30: #1 total tags in treatment: 32166857 INFO @ Sun, 21 Jun 2020 22:27:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:30: #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 22:27:31: #1 tags after filtering in treatment: 32166812 INFO @ Sun, 21 Jun 2020 22:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:27:32: 27000000 INFO @ Sun, 21 Jun 2020 22:27:33: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 22:27:33: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 22:27:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:27:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:27:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:27:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:27:33: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:27:33: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 21 Jun 2020 22:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.10_model.r WARNING @ Sun, 21 Jun 2020 22:27:33: #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 22:27:33: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 21 Jun 2020 22:27:33: #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 22:27:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:27:37: 28000000 INFO @ Sun, 21 Jun 2020 22:27:42: 29000000 INFO @ Sun, 21 Jun 2020 22:27:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:27:47: 30000000 INFO @ Sun, 21 Jun 2020 22:27:52: 31000000 INFO @ Sun, 21 Jun 2020 22:27:57: 32000000 INFO @ Sun, 21 Jun 2020 22:27:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:27:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:27:58: #1 total tags in treatment: 32166857 INFO @ Sun, 21 Jun 2020 22:27:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:58: #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 22:27:58: #1 tags after filtering in treatment: 32166812 INFO @ Sun, 21 Jun 2020 22:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:28:00: #2 number of paired peaks: 433 WARNING @ Sun, 21 Jun 2020 22:28:00: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sun, 21 Jun 2020 22:28:00: start model_add_line... INFO @ Sun, 21 Jun 2020 22:28:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:28:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:28:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:28:01: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:28:01: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 21 Jun 2020 22:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.20_model.r WARNING @ Sun, 21 Jun 2020 22:28:01: #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 22:28:01: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 21 Jun 2020 22:28:01: #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 22:28:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:28:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.05_summits.bed INFO @ Sun, 21 Jun 2020 22:28:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:28:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.10_summits.bed INFO @ Sun, 21 Jun 2020 22:28:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:28:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:29:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:29:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:29:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436062/SRX5436062.20_summits.bed INFO @ Sun, 21 Jun 2020 22:29:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling