Job ID = 6454349 SRX = SRX201885 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:10:39 prefetch.2.10.7: 1) Downloading 'SRR609675'... 2020-06-21T09:10:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:18:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:18:01 prefetch.2.10.7: 1) 'SRR609675' was downloaded successfully Read 34978622 spots for SRR609675/SRR609675.sra Written 34978622 spots for SRR609675/SRR609675.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: 00:15:21 34978622 reads; of these: 34978622 (100.00%) were unpaired; of these: 911153 (2.60%) aligned 0 times 9090817 (25.99%) aligned exactly 1 time 24976652 (71.41%) aligned >1 times 97.40% overall alignment rate Time searching: 00:15:22 Overall time: 00:15:22 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] 14983001 / 34067469 = 0.4398 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 18:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.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 18:44:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:44: 1000000 INFO @ Sun, 21 Jun 2020 18:44:49: 2000000 INFO @ Sun, 21 Jun 2020 18:44:55: 3000000 INFO @ Sun, 21 Jun 2020 18:45:01: 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 18:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.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 18:45:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:08: 5000000 INFO @ Sun, 21 Jun 2020 18:45:15: 6000000 INFO @ Sun, 21 Jun 2020 18:45:15: 1000000 INFO @ Sun, 21 Jun 2020 18:45:21: 7000000 INFO @ Sun, 21 Jun 2020 18:45:21: 2000000 INFO @ Sun, 21 Jun 2020 18:45:28: 8000000 INFO @ Sun, 21 Jun 2020 18:45:28: 3000000 INFO @ Sun, 21 Jun 2020 18:45:35: 9000000 INFO @ Sun, 21 Jun 2020 18:45:35: 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 18:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.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 18:45:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:42: 10000000 INFO @ Sun, 21 Jun 2020 18:45:42: 5000000 INFO @ Sun, 21 Jun 2020 18:45:45: 1000000 INFO @ Sun, 21 Jun 2020 18:45:48: 11000000 INFO @ Sun, 21 Jun 2020 18:45:49: 6000000 INFO @ Sun, 21 Jun 2020 18:45:52: 2000000 INFO @ Sun, 21 Jun 2020 18:45:55: 12000000 INFO @ Sun, 21 Jun 2020 18:45:56: 7000000 INFO @ Sun, 21 Jun 2020 18:45:59: 3000000 INFO @ Sun, 21 Jun 2020 18:46:02: 13000000 INFO @ Sun, 21 Jun 2020 18:46:03: 8000000 INFO @ Sun, 21 Jun 2020 18:46:06: 4000000 INFO @ Sun, 21 Jun 2020 18:46:10: 14000000 INFO @ Sun, 21 Jun 2020 18:46:10: 9000000 INFO @ Sun, 21 Jun 2020 18:46:13: 5000000 INFO @ Sun, 21 Jun 2020 18:46:16: 15000000 INFO @ Sun, 21 Jun 2020 18:46:17: 10000000 INFO @ Sun, 21 Jun 2020 18:46:20: 6000000 INFO @ Sun, 21 Jun 2020 18:46:23: 16000000 INFO @ Sun, 21 Jun 2020 18:46:23: 11000000 INFO @ Sun, 21 Jun 2020 18:46:26: 7000000 INFO @ Sun, 21 Jun 2020 18:46:30: 17000000 INFO @ Sun, 21 Jun 2020 18:46:30: 12000000 INFO @ Sun, 21 Jun 2020 18:46:33: 8000000 INFO @ Sun, 21 Jun 2020 18:46:37: 13000000 INFO @ Sun, 21 Jun 2020 18:46:37: 18000000 INFO @ Sun, 21 Jun 2020 18:46:40: 9000000 INFO @ Sun, 21 Jun 2020 18:46:44: 19000000 INFO @ Sun, 21 Jun 2020 18:46:44: 14000000 INFO @ Sun, 21 Jun 2020 18:46:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:46:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:46:45: #1 total tags in treatment: 19084468 INFO @ Sun, 21 Jun 2020 18:46:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:45: #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 18:46:45: #1 tags after filtering in treatment: 19084436 INFO @ Sun, 21 Jun 2020 18:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:47: 10000000 INFO @ Sun, 21 Jun 2020 18:46:47: #2 number of paired peaks: 6210 INFO @ Sun, 21 Jun 2020 18:46:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:48: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 18:46:48: #2 alternative fragment length(s) may be 2,61 bps INFO @ Sun, 21 Jun 2020 18:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.05_model.r WARNING @ Sun, 21 Jun 2020 18:46:48: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:48: #2 You may need to consider one of the other alternative d(s): 2,61 WARNING @ Sun, 21 Jun 2020 18:46:48: #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 18:46:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:51: 15000000 INFO @ Sun, 21 Jun 2020 18:46:53: 11000000 INFO @ Sun, 21 Jun 2020 18:46:57: 16000000 INFO @ Sun, 21 Jun 2020 18:47:00: 12000000 INFO @ Sun, 21 Jun 2020 18:47:04: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:47:06: 13000000 INFO @ Sun, 21 Jun 2020 18:47:10: 18000000 INFO @ Sun, 21 Jun 2020 18:47:13: 14000000 INFO @ Sun, 21 Jun 2020 18:47:17: 19000000 INFO @ Sun, 21 Jun 2020 18:47:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:47:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:47:17: #1 total tags in treatment: 19084468 INFO @ Sun, 21 Jun 2020 18:47:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:17: #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 18:47:18: #1 tags after filtering in treatment: 19084436 INFO @ Sun, 21 Jun 2020 18:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:19: 15000000 INFO @ Sun, 21 Jun 2020 18:47:20: #2 number of paired peaks: 6210 INFO @ Sun, 21 Jun 2020 18:47:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:20: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 18:47:20: #2 alternative fragment length(s) may be 2,61 bps INFO @ Sun, 21 Jun 2020 18:47:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.10_model.r WARNING @ Sun, 21 Jun 2020 18:47:20: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:20: #2 You may need to consider one of the other alternative d(s): 2,61 WARNING @ Sun, 21 Jun 2020 18:47:20: #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 18:47:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:24: 16000000 INFO @ Sun, 21 Jun 2020 18:47:30: 17000000 INFO @ Sun, 21 Jun 2020 18:47:36: 18000000 INFO @ Sun, 21 Jun 2020 18:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.05_summits.bed INFO @ Sun, 21 Jun 2020 18:47:40: Done! pass1 - making usageList (1237 chroms): 3 millis pass2 - checking and writing primary data (9594 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:47:41: 19000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:47:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:47:42: #1 total tags in treatment: 19084468 INFO @ Sun, 21 Jun 2020 18:47:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:42: #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 18:47:43: #1 tags after filtering in treatment: 19084436 INFO @ Sun, 21 Jun 2020 18:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:45: #2 number of paired peaks: 6210 INFO @ Sun, 21 Jun 2020 18:47:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:45: #2 predicted fragment length is 61 bps INFO @ Sun, 21 Jun 2020 18:47:45: #2 alternative fragment length(s) may be 2,61 bps INFO @ Sun, 21 Jun 2020 18:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.20_model.r WARNING @ Sun, 21 Jun 2020 18:47:45: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:45: #2 You may need to consider one of the other alternative d(s): 2,61 WARNING @ Sun, 21 Jun 2020 18:47:45: #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 18:47:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:11: Done! pass1 - making usageList (1073 chroms): 2 millis pass2 - checking and writing primary data (4547 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201885/SRX201885.20_summits.bed INFO @ Sun, 21 Jun 2020 18:48:35: Done! pass1 - making usageList (809 chroms): 2 millis pass2 - checking and writing primary data (2626 records, 4 fields): 45 millis CompletedMACS2peakCalling