Job ID = 6453625 SRX = SRX1300694 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:26:56 prefetch.2.10.7: 1) Downloading 'SRR2548370'... 2020-06-21T08:26:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:47 prefetch.2.10.7: 1) 'SRR2548370' was downloaded successfully Read 21046604 spots for SRR2548370/SRR2548370.sra Written 21046604 spots for SRR2548370/SRR2548370.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: 00:05:49 21046604 reads; of these: 21046604 (100.00%) were unpaired; of these: 1003870 (4.77%) aligned 0 times 14212801 (67.53%) aligned exactly 1 time 5829933 (27.70%) aligned >1 times 95.23% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 2596014 / 20042734 = 0.1295 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 17:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.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 17:41:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:41:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:41:56: 1000000 INFO @ Sun, 21 Jun 2020 17:42:02: 2000000 INFO @ Sun, 21 Jun 2020 17:42:08: 3000000 INFO @ Sun, 21 Jun 2020 17:42:14: 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 17:42:20: 5000000 INFO @ Sun, 21 Jun 2020 17:42:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.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 17:42:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:26: 6000000 INFO @ Sun, 21 Jun 2020 17:42:27: 1000000 INFO @ Sun, 21 Jun 2020 17:42:33: 7000000 INFO @ Sun, 21 Jun 2020 17:42:34: 2000000 INFO @ Sun, 21 Jun 2020 17:42:40: 8000000 INFO @ Sun, 21 Jun 2020 17:42:41: 3000000 INFO @ Sun, 21 Jun 2020 17:42:46: 9000000 INFO @ Sun, 21 Jun 2020 17:42:48: 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 17:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.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 17:42:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:42:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:42:53: 10000000 INFO @ Sun, 21 Jun 2020 17:42:55: 5000000 INFO @ Sun, 21 Jun 2020 17:43:00: 11000000 INFO @ Sun, 21 Jun 2020 17:43:00: 1000000 INFO @ Sun, 21 Jun 2020 17:43:02: 6000000 INFO @ Sun, 21 Jun 2020 17:43:08: 12000000 INFO @ Sun, 21 Jun 2020 17:43:08: 2000000 INFO @ Sun, 21 Jun 2020 17:43:09: 7000000 INFO @ Sun, 21 Jun 2020 17:43:15: 13000000 INFO @ Sun, 21 Jun 2020 17:43:16: 3000000 INFO @ Sun, 21 Jun 2020 17:43:17: 8000000 INFO @ Sun, 21 Jun 2020 17:43:23: 14000000 INFO @ Sun, 21 Jun 2020 17:43:24: 4000000 INFO @ Sun, 21 Jun 2020 17:43:24: 9000000 INFO @ Sun, 21 Jun 2020 17:43:30: 15000000 INFO @ Sun, 21 Jun 2020 17:43:32: 10000000 INFO @ Sun, 21 Jun 2020 17:43:32: 5000000 INFO @ Sun, 21 Jun 2020 17:43:37: 16000000 INFO @ Sun, 21 Jun 2020 17:43:39: 11000000 INFO @ Sun, 21 Jun 2020 17:43:40: 6000000 INFO @ Sun, 21 Jun 2020 17:43:45: 17000000 INFO @ Sun, 21 Jun 2020 17:43:46: 12000000 INFO @ Sun, 21 Jun 2020 17:43:47: 7000000 INFO @ Sun, 21 Jun 2020 17:43:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:43:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:43:48: #1 total tags in treatment: 17446720 INFO @ Sun, 21 Jun 2020 17:43:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:43:48: #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 17:43:49: #1 tags after filtering in treatment: 17446720 INFO @ Sun, 21 Jun 2020 17:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:43:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:43:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:43:50: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 17:43:50: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 17:43:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:43:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:43:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:43:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:43:50: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:43:50: #2 alternative fragment length(s) may be 2,43,553,579 bps INFO @ Sun, 21 Jun 2020 17:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.05_model.r WARNING @ Sun, 21 Jun 2020 17:43:50: #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 17:43:50: #2 You may need to consider one of the other alternative d(s): 2,43,553,579 WARNING @ Sun, 21 Jun 2020 17:43:50: #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 17:43:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:43:53: 13000000 INFO @ Sun, 21 Jun 2020 17:43:55: 8000000 INFO @ Sun, 21 Jun 2020 17:44:01: 14000000 INFO @ Sun, 21 Jun 2020 17:44:02: 9000000 INFO @ Sun, 21 Jun 2020 17:44:08: 15000000 INFO @ Sun, 21 Jun 2020 17:44:10: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:44:15: 16000000 INFO @ Sun, 21 Jun 2020 17:44:18: 11000000 INFO @ Sun, 21 Jun 2020 17:44:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:22: 17000000 INFO @ Sun, 21 Jun 2020 17:44:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:44:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:44:25: #1 total tags in treatment: 17446720 INFO @ Sun, 21 Jun 2020 17:44:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:25: #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 17:44:26: 12000000 INFO @ Sun, 21 Jun 2020 17:44:26: #1 tags after filtering in treatment: 17446720 INFO @ Sun, 21 Jun 2020 17:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:27: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 17:44:27: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 17:44:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:27: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:44:27: #2 alternative fragment length(s) may be 2,43,553,579 bps INFO @ Sun, 21 Jun 2020 17:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.10_model.r WARNING @ Sun, 21 Jun 2020 17:44:27: #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 17:44:27: #2 You may need to consider one of the other alternative d(s): 2,43,553,579 WARNING @ Sun, 21 Jun 2020 17:44:27: #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 17:44:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:44:33: 13000000 INFO @ Sun, 21 Jun 2020 17:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.05_summits.bed INFO @ Sun, 21 Jun 2020 17:44:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:44:41: 14000000 INFO @ Sun, 21 Jun 2020 17:44:48: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:44:55: 16000000 INFO @ Sun, 21 Jun 2020 17:44:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:02: 17000000 INFO @ Sun, 21 Jun 2020 17:45:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:05: #1 total tags in treatment: 17446720 INFO @ Sun, 21 Jun 2020 17:45:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:05: #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 17:45:06: #1 tags after filtering in treatment: 17446720 INFO @ Sun, 21 Jun 2020 17:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:06: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:07: #2 number of paired peaks: 559 WARNING @ Sun, 21 Jun 2020 17:45:07: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:07: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 17:45:07: #2 alternative fragment length(s) may be 2,43,553,579 bps INFO @ Sun, 21 Jun 2020 17:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.20_model.r WARNING @ Sun, 21 Jun 2020 17:45:07: #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 17:45:07: #2 You may need to consider one of the other alternative d(s): 2,43,553,579 WARNING @ Sun, 21 Jun 2020 17:45:07: #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 17:45:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.10_summits.bed INFO @ Sun, 21 Jun 2020 17:45:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:45:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300694/SRX1300694.20_summits.bed INFO @ Sun, 21 Jun 2020 17:45:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling