Job ID = 6453633 SRX = SRX1308482 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:24:47 prefetch.2.10.7: 1) Downloading 'SRR2566777'... 2020-06-21T08:24:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:26:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:26:30 prefetch.2.10.7: 'SRR2566777' is valid 2020-06-21T08:26:30 prefetch.2.10.7: 1) 'SRR2566777' was downloaded successfully Read 7910274 spots for SRR2566777/SRR2566777.sra Written 7910274 spots for SRR2566777/SRR2566777.sra 2020-06-21T08:27:03 prefetch.2.10.7: 1) Downloading 'SRR2566778'... 2020-06-21T08:27:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:31 prefetch.2.10.7: 'SRR2566778' is valid 2020-06-21T08:29:31 prefetch.2.10.7: 1) 'SRR2566778' was downloaded successfully Read 7912825 spots for SRR2566778/SRR2566778.sra Written 7912825 spots for SRR2566778/SRR2566778.sra 2020-06-21T08:30:06 prefetch.2.10.7: 1) Downloading 'SRR2566779'... 2020-06-21T08:30:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:33 prefetch.2.10.7: 'SRR2566779' is valid 2020-06-21T08:32:33 prefetch.2.10.7: 1) 'SRR2566779' was downloaded successfully Read 9889708 spots for SRR2566779/SRR2566779.sra Written 9889708 spots for SRR2566779/SRR2566779.sra 2020-06-21T08:33:12 prefetch.2.10.7: 1) Downloading 'SRR2566780'... 2020-06-21T08:33:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:33 prefetch.2.10.7: 'SRR2566780' is valid 2020-06-21T08:36:33 prefetch.2.10.7: 1) 'SRR2566780' was downloaded successfully Read 9887697 spots for SRR2566780/SRR2566780.sra Written 9887697 spots for SRR2566780/SRR2566780.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: 00:09:06 35600504 reads; of these: 35600504 (100.00%) were unpaired; of these: 3240260 (9.10%) aligned 0 times 25621258 (71.97%) aligned exactly 1 time 6738986 (18.93%) aligned >1 times 90.90% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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] 25550853 / 32360244 = 0.7896 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 17:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.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 17:52:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:20: 1000000 INFO @ Sun, 21 Jun 2020 17:52:25: 2000000 INFO @ Sun, 21 Jun 2020 17:52:31: 3000000 INFO @ Sun, 21 Jun 2020 17:52:37: 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 17:52:43: 5000000 INFO @ Sun, 21 Jun 2020 17:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.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 17:52:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:50: 6000000 INFO @ Sun, 21 Jun 2020 17:52:50: 1000000 INFO @ Sun, 21 Jun 2020 17:52:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:52:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:52:55: #1 total tags in treatment: 6809391 INFO @ Sun, 21 Jun 2020 17:52:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:55: #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 17:52:56: #1 tags after filtering in treatment: 6809375 INFO @ Sun, 21 Jun 2020 17:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:56: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 17:52:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:57: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 17:52:57: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 17:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.05_model.r WARNING @ Sun, 21 Jun 2020 17:52:57: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:57: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 17:52:57: #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 17:52:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:52:57: 2000000 INFO @ Sun, 21 Jun 2020 17:53:03: 3000000 INFO @ Sun, 21 Jun 2020 17:53:09: 4000000 INFO @ Sun, 21 Jun 2020 17:53:11: #3 Call peaks for each chromosome... 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 17:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.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 17:53:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:15: 5000000 INFO @ Sun, 21 Jun 2020 17:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.05_summits.bed INFO @ Sun, 21 Jun 2020 17:53:17: Done! pass1 - making usageList (696 chroms): 1 millis pass2 - checking and writing primary data (4732 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:21: 1000000 INFO @ Sun, 21 Jun 2020 17:53:23: 6000000 INFO @ Sun, 21 Jun 2020 17:53:27: 2000000 INFO @ Sun, 21 Jun 2020 17:53:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:28: #1 total tags in treatment: 6809391 INFO @ Sun, 21 Jun 2020 17:53:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:28: #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 17:53:29: #1 tags after filtering in treatment: 6809375 INFO @ Sun, 21 Jun 2020 17:53:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:29: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 17:53:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:29: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 17:53:29: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 17:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.10_model.r WARNING @ Sun, 21 Jun 2020 17:53:29: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:29: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 17:53:29: #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 17:53:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:34: 3000000 INFO @ Sun, 21 Jun 2020 17:53:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:53:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:46: 5000000 INFO @ Sun, 21 Jun 2020 17:53:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.10_summits.bed INFO @ Sun, 21 Jun 2020 17:53:51: Done! pass1 - making usageList (513 chroms): 2 millis pass2 - checking and writing primary data (2470 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:52: 6000000 INFO @ Sun, 21 Jun 2020 17:53:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:57: #1 total tags in treatment: 6809391 INFO @ Sun, 21 Jun 2020 17:53:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:57: #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 17:53:58: #1 tags after filtering in treatment: 6809375 INFO @ Sun, 21 Jun 2020 17:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:58: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 17:53:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:58: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 17:53:58: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 17:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:58: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:58: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sun, 21 Jun 2020 17:53:58: #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 17:53:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308482/SRX1308482.20_summits.bed INFO @ Sun, 21 Jun 2020 17:54:19: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1608 records, 4 fields): 14 millis CompletedMACS2peakCalling