Job ID = 6455225 SRX = SRX287570 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:55 prefetch.2.10.7: 1) Downloading 'SRR869713'... 2020-06-21T09:53:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:56:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:56:32 prefetch.2.10.7: 'SRR869713' is valid 2020-06-21T09:56:32 prefetch.2.10.7: 1) 'SRR869713' was downloaded successfully Read 14916545 spots for SRR869713/SRR869713.sra Written 14916545 spots for SRR869713/SRR869713.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: 00:04:44 14916545 reads; of these: 14916545 (100.00%) were unpaired; of these: 1177082 (7.89%) aligned 0 times 8826016 (59.17%) aligned exactly 1 time 4913447 (32.94%) aligned >1 times 92.11% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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] 4520936 / 13739463 = 0.3290 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 19:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.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 19:05:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:44: 1000000 INFO @ Sun, 21 Jun 2020 19:05:48: 2000000 INFO @ Sun, 21 Jun 2020 19:05:53: 3000000 INFO @ Sun, 21 Jun 2020 19:05:57: 4000000 INFO @ Sun, 21 Jun 2020 19:06:02: 5000000 INFO @ Sun, 21 Jun 2020 19:06:07: 6000000 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 19:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.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 19:06:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:11: 7000000 INFO @ Sun, 21 Jun 2020 19:06:14: 1000000 INFO @ Sun, 21 Jun 2020 19:06:16: 8000000 INFO @ Sun, 21 Jun 2020 19:06:18: 2000000 INFO @ Sun, 21 Jun 2020 19:06:21: 9000000 INFO @ Sun, 21 Jun 2020 19:06:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:22: #1 total tags in treatment: 9218527 INFO @ Sun, 21 Jun 2020 19:06:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:22: #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 19:06:23: #1 tags after filtering in treatment: 9218526 INFO @ Sun, 21 Jun 2020 19:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:23: 3000000 INFO @ Sun, 21 Jun 2020 19:06:23: #2 number of paired peaks: 1034 INFO @ Sun, 21 Jun 2020 19:06:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:23: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:06:23: #2 alternative fragment length(s) may be 4,42,557 bps INFO @ Sun, 21 Jun 2020 19:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.05_model.r WARNING @ Sun, 21 Jun 2020 19:06:23: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:06:23: #2 You may need to consider one of the other alternative d(s): 4,42,557 WARNING @ Sun, 21 Jun 2020 19:06:23: #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 19:06:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:28: 4000000 INFO @ Sun, 21 Jun 2020 19:06:32: 5000000 INFO @ Sun, 21 Jun 2020 19:06:37: 6000000 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 19:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.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 19:06:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:06:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:06:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:42: 7000000 INFO @ Sun, 21 Jun 2020 19:06:44: 1000000 INFO @ Sun, 21 Jun 2020 19:06:47: 8000000 INFO @ Sun, 21 Jun 2020 19:06:48: 2000000 INFO @ Sun, 21 Jun 2020 19:06:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.05_summits.bed INFO @ Sun, 21 Jun 2020 19:06:51: Done! pass1 - making usageList (606 chroms): 1 millis pass2 - checking and writing primary data (2192 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:52: 9000000 INFO @ Sun, 21 Jun 2020 19:06:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:06:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:06:53: #1 total tags in treatment: 9218527 INFO @ Sun, 21 Jun 2020 19:06:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:06:53: #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 19:06:53: #1 tags after filtering in treatment: 9218526 INFO @ Sun, 21 Jun 2020 19:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:06:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:06:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:06:53: 3000000 INFO @ Sun, 21 Jun 2020 19:06:54: #2 number of paired peaks: 1034 INFO @ Sun, 21 Jun 2020 19:06:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:06:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:06:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:06:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:06:54: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:06:54: #2 alternative fragment length(s) may be 4,42,557 bps INFO @ Sun, 21 Jun 2020 19:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.10_model.r WARNING @ Sun, 21 Jun 2020 19:06:54: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:06:54: #2 You may need to consider one of the other alternative d(s): 4,42,557 WARNING @ Sun, 21 Jun 2020 19:06:54: #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 19:06:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:06:58: 4000000 INFO @ Sun, 21 Jun 2020 19:07:03: 5000000 INFO @ Sun, 21 Jun 2020 19:07:07: 6000000 INFO @ Sun, 21 Jun 2020 19:07:12: 7000000 INFO @ Sun, 21 Jun 2020 19:07:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:17: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:07:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.10_summits.bed INFO @ Sun, 21 Jun 2020 19:07:21: Done! INFO @ Sun, 21 Jun 2020 19:07:22: 9000000 pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1933 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:07:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:07:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:07:23: #1 total tags in treatment: 9218527 INFO @ Sun, 21 Jun 2020 19:07:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:07:23: #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 19:07:23: #1 tags after filtering in treatment: 9218526 INFO @ Sun, 21 Jun 2020 19:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:07:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:07:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:07:24: #2 number of paired peaks: 1034 INFO @ Sun, 21 Jun 2020 19:07:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:07:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:07:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:07:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:07:24: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:07:24: #2 alternative fragment length(s) may be 4,42,557 bps INFO @ Sun, 21 Jun 2020 19:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.20_model.r WARNING @ Sun, 21 Jun 2020 19:07:24: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:07:24: #2 You may need to consider one of the other alternative d(s): 4,42,557 WARNING @ Sun, 21 Jun 2020 19:07:24: #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 19:07:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:07:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:07:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287570/SRX287570.20_summits.bed INFO @ Sun, 21 Jun 2020 19:07:51: Done! pass1 - making usageList (381 chroms): 1 millis pass2 - checking and writing primary data (907 records, 4 fields): 12 millis CompletedMACS2peakCalling