Job ID = 6454351 SRX = SRX201887 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:54 prefetch.2.10.7: 1) Downloading 'SRR609677'... 2020-06-21T09:15:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:25:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:25:10 prefetch.2.10.7: 1) 'SRR609677' was downloaded successfully Read 41417081 spots for SRR609677/SRR609677.sra Written 41417081 spots for SRR609677/SRR609677.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:11 41417081 reads; of these: 41417081 (100.00%) were unpaired; of these: 1063653 (2.57%) aligned 0 times 12290373 (29.67%) aligned exactly 1 time 28063055 (67.76%) aligned >1 times 97.43% overall alignment rate Time searching: 00:18:12 Overall time: 00:18:12 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] 16456338 / 40353428 = 0.4078 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 18:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.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 18:55:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:19: 1000000 INFO @ Sun, 21 Jun 2020 18:55:25: 2000000 INFO @ Sun, 21 Jun 2020 18:55:31: 3000000 INFO @ Sun, 21 Jun 2020 18:55:36: 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 18:55:42: 5000000 INFO @ Sun, 21 Jun 2020 18:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.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 18:55:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:48: 6000000 INFO @ Sun, 21 Jun 2020 18:55:50: 1000000 INFO @ Sun, 21 Jun 2020 18:55:54: 7000000 INFO @ Sun, 21 Jun 2020 18:55:56: 2000000 INFO @ Sun, 21 Jun 2020 18:56:00: 8000000 INFO @ Sun, 21 Jun 2020 18:56:02: 3000000 INFO @ Sun, 21 Jun 2020 18:56:06: 9000000 INFO @ Sun, 21 Jun 2020 18:56:08: 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 18:56:13: 10000000 INFO @ Sun, 21 Jun 2020 18:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.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 18:56:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:14: 5000000 INFO @ Sun, 21 Jun 2020 18:56:19: 11000000 INFO @ Sun, 21 Jun 2020 18:56:20: 1000000 INFO @ Sun, 21 Jun 2020 18:56:21: 6000000 INFO @ Sun, 21 Jun 2020 18:56:25: 12000000 INFO @ Sun, 21 Jun 2020 18:56:26: 2000000 INFO @ Sun, 21 Jun 2020 18:56:27: 7000000 INFO @ Sun, 21 Jun 2020 18:56:31: 13000000 INFO @ Sun, 21 Jun 2020 18:56:32: 3000000 INFO @ Sun, 21 Jun 2020 18:56:33: 8000000 INFO @ Sun, 21 Jun 2020 18:56:37: 14000000 INFO @ Sun, 21 Jun 2020 18:56:38: 4000000 INFO @ Sun, 21 Jun 2020 18:56:39: 9000000 INFO @ Sun, 21 Jun 2020 18:56:44: 15000000 INFO @ Sun, 21 Jun 2020 18:56:44: 5000000 INFO @ Sun, 21 Jun 2020 18:56:46: 10000000 INFO @ Sun, 21 Jun 2020 18:56:50: 16000000 INFO @ Sun, 21 Jun 2020 18:56:51: 6000000 INFO @ Sun, 21 Jun 2020 18:56:52: 11000000 INFO @ Sun, 21 Jun 2020 18:56:56: 17000000 INFO @ Sun, 21 Jun 2020 18:56:57: 7000000 INFO @ Sun, 21 Jun 2020 18:56:58: 12000000 INFO @ Sun, 21 Jun 2020 18:57:03: 18000000 INFO @ Sun, 21 Jun 2020 18:57:03: 8000000 INFO @ Sun, 21 Jun 2020 18:57:04: 13000000 INFO @ Sun, 21 Jun 2020 18:57:09: 19000000 INFO @ Sun, 21 Jun 2020 18:57:10: 9000000 INFO @ Sun, 21 Jun 2020 18:57:11: 14000000 INFO @ Sun, 21 Jun 2020 18:57:15: 20000000 INFO @ Sun, 21 Jun 2020 18:57:16: 10000000 INFO @ Sun, 21 Jun 2020 18:57:17: 15000000 INFO @ Sun, 21 Jun 2020 18:57:22: 21000000 INFO @ Sun, 21 Jun 2020 18:57:22: 11000000 INFO @ Sun, 21 Jun 2020 18:57:23: 16000000 INFO @ Sun, 21 Jun 2020 18:57:28: 22000000 INFO @ Sun, 21 Jun 2020 18:57:28: 12000000 INFO @ Sun, 21 Jun 2020 18:57:30: 17000000 INFO @ Sun, 21 Jun 2020 18:57:34: 13000000 INFO @ Sun, 21 Jun 2020 18:57:34: 23000000 INFO @ Sun, 21 Jun 2020 18:57:36: 18000000 INFO @ Sun, 21 Jun 2020 18:57:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:40: #1 total tags in treatment: 23897090 INFO @ Sun, 21 Jun 2020 18:57:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:40: #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 18:57:40: 14000000 INFO @ Sun, 21 Jun 2020 18:57:41: #1 tags after filtering in treatment: 23897059 INFO @ Sun, 21 Jun 2020 18:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:43: #2 number of paired peaks: 4541 INFO @ Sun, 21 Jun 2020 18:57:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:43: 19000000 INFO @ Sun, 21 Jun 2020 18:57:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:43: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:57:43: #2 alternative fragment length(s) may be 1,48 bps INFO @ Sun, 21 Jun 2020 18:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.05_model.r WARNING @ Sun, 21 Jun 2020 18:57:43: #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 18:57:43: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Sun, 21 Jun 2020 18:57:43: #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 18:57:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:57:47: 15000000 INFO @ Sun, 21 Jun 2020 18:57:49: 20000000 INFO @ Sun, 21 Jun 2020 18:57:53: 16000000 INFO @ Sun, 21 Jun 2020 18:57:55: 21000000 INFO @ Sun, 21 Jun 2020 18:57:59: 17000000 INFO @ Sun, 21 Jun 2020 18:58:02: 22000000 INFO @ Sun, 21 Jun 2020 18:58:06: 18000000 INFO @ Sun, 21 Jun 2020 18:58:08: 23000000 INFO @ Sun, 21 Jun 2020 18:58:12: 19000000 INFO @ Sun, 21 Jun 2020 18:58:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:14: #1 total tags in treatment: 23897090 INFO @ Sun, 21 Jun 2020 18:58:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:14: #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 18:58:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:14: #1 tags after filtering in treatment: 23897059 INFO @ Sun, 21 Jun 2020 18:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:16: #2 number of paired peaks: 4541 INFO @ Sun, 21 Jun 2020 18:58:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:17: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:58:17: #2 alternative fragment length(s) may be 1,48 bps INFO @ Sun, 21 Jun 2020 18:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.10_model.r WARNING @ Sun, 21 Jun 2020 18:58:17: #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 18:58:17: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Sun, 21 Jun 2020 18:58:17: #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 18:58:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:18: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:24: 21000000 INFO @ Sun, 21 Jun 2020 18:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.05_summits.bed INFO @ Sun, 21 Jun 2020 18:58:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:30: 22000000 INFO @ Sun, 21 Jun 2020 18:58:36: 23000000 INFO @ Sun, 21 Jun 2020 18:58:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:41: #1 total tags in treatment: 23897090 INFO @ Sun, 21 Jun 2020 18:58:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:41: #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 18:58:42: #1 tags after filtering in treatment: 23897059 INFO @ Sun, 21 Jun 2020 18:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:42: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:44: #2 number of paired peaks: 4541 INFO @ Sun, 21 Jun 2020 18:58:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:44: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:58:44: #2 alternative fragment length(s) may be 1,48 bps INFO @ Sun, 21 Jun 2020 18:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.20_model.r WARNING @ Sun, 21 Jun 2020 18:58:44: #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 18:58:44: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Sun, 21 Jun 2020 18:58:44: #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 18:58:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201887/SRX201887.20_summits.bed INFO @ Sun, 21 Jun 2020 18:59:30: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling