Job ID = 6453357 SRX = SRX1120691 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:26 prefetch.2.10.7: 1) Downloading 'SRR2129923'... 2020-06-21T08:28:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:34 prefetch.2.10.7: 1) 'SRR2129923' was downloaded successfully Read 15690855 spots for SRR2129923/SRR2129923.sra Written 15690855 spots for SRR2129923/SRR2129923.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: 00:07:25 15690855 reads; of these: 15690855 (100.00%) were unpaired; of these: 1150589 (7.33%) aligned 0 times 4697176 (29.94%) aligned exactly 1 time 9843090 (62.73%) aligned >1 times 92.67% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 8 files... [bam_rmdupse_core] 4889383 / 14540266 = 0.3363 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 17:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.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 17:45:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:26: 1000000 INFO @ Sun, 21 Jun 2020 17:45:32: 2000000 INFO @ Sun, 21 Jun 2020 17:45:39: 3000000 INFO @ Sun, 21 Jun 2020 17:45:45: 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 17:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.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 17:45:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:51: 5000000 INFO @ Sun, 21 Jun 2020 17:45:56: 1000000 INFO @ Sun, 21 Jun 2020 17:45:58: 6000000 INFO @ Sun, 21 Jun 2020 17:46:02: 2000000 INFO @ Sun, 21 Jun 2020 17:46:05: 7000000 INFO @ Sun, 21 Jun 2020 17:46:09: 3000000 INFO @ Sun, 21 Jun 2020 17:46:12: 8000000 INFO @ Sun, 21 Jun 2020 17:46:16: 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 17:46:18: 9000000 INFO @ Sun, 21 Jun 2020 17:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.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 17:46:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:23: 5000000 INFO @ Sun, 21 Jun 2020 17:46:23: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:46:23: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:46:23: #1 total tags in treatment: 9650883 INFO @ Sun, 21 Jun 2020 17:46:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:23: #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 17:46:24: #1 tags after filtering in treatment: 9650820 INFO @ Sun, 21 Jun 2020 17:46:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:25: #2 number of paired peaks: 5856 INFO @ Sun, 21 Jun 2020 17:46:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:25: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 17:46:25: #2 alternative fragment length(s) may be 2,84 bps INFO @ Sun, 21 Jun 2020 17:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.05_model.r WARNING @ Sun, 21 Jun 2020 17:46:25: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:25: #2 You may need to consider one of the other alternative d(s): 2,84 WARNING @ Sun, 21 Jun 2020 17:46:25: #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 17:46:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:27: 1000000 INFO @ Sun, 21 Jun 2020 17:46:30: 6000000 INFO @ Sun, 21 Jun 2020 17:46:35: 2000000 INFO @ Sun, 21 Jun 2020 17:46:37: 7000000 INFO @ Sun, 21 Jun 2020 17:46:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:44: 3000000 INFO @ Sun, 21 Jun 2020 17:46:45: 8000000 INFO @ Sun, 21 Jun 2020 17:46:52: 4000000 INFO @ Sun, 21 Jun 2020 17:46:52: 9000000 INFO @ Sun, 21 Jun 2020 17:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.05_summits.bed INFO @ Sun, 21 Jun 2020 17:46:53: Done! pass1 - making usageList (1055 chroms): 1 millis pass2 - checking and writing primary data (4720 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:46:57: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:46:57: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:46:57: #1 total tags in treatment: 9650883 INFO @ Sun, 21 Jun 2020 17:46:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:57: #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 17:46:57: #1 tags after filtering in treatment: 9650820 INFO @ Sun, 21 Jun 2020 17:46:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:58: #2 number of paired peaks: 5856 INFO @ Sun, 21 Jun 2020 17:46:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:58: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 17:46:58: #2 alternative fragment length(s) may be 2,84 bps INFO @ Sun, 21 Jun 2020 17:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.10_model.r WARNING @ Sun, 21 Jun 2020 17:46:59: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:59: #2 You may need to consider one of the other alternative d(s): 2,84 WARNING @ Sun, 21 Jun 2020 17:46:59: #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 17:46:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:00: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:47:07: 6000000 INFO @ Sun, 21 Jun 2020 17:47:15: 7000000 INFO @ Sun, 21 Jun 2020 17:47:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:47:23: 8000000 INFO @ Sun, 21 Jun 2020 17:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:26: Done! INFO @ Sun, 21 Jun 2020 17:47:30: 9000000 pass1 - making usageList (829 chroms): 1 millis pass2 - checking and writing primary data (2530 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:35: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:47:35: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:47:35: #1 total tags in treatment: 9650883 INFO @ Sun, 21 Jun 2020 17:47:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:35: #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 17:47:36: #1 tags after filtering in treatment: 9650820 INFO @ Sun, 21 Jun 2020 17:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:36: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:37: #2 number of paired peaks: 5856 INFO @ Sun, 21 Jun 2020 17:47:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:37: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:37: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:37: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 17:47:37: #2 alternative fragment length(s) may be 2,84 bps INFO @ Sun, 21 Jun 2020 17:47:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.20_model.r WARNING @ Sun, 21 Jun 2020 17:47:37: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:37: #2 You may need to consider one of the other alternative d(s): 2,84 WARNING @ Sun, 21 Jun 2020 17:47:37: #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 17:47:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120691/SRX1120691.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:06: Done! pass1 - making usageList (629 chroms): 1 millis pass2 - checking and writing primary data (1594 records, 4 fields): 18 millis CompletedMACS2peakCalling