Job ID = 8184319 SRX = SRX8047587 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:16:12 prefetch.2.10.7: 1) Downloading 'SRR11471312'... 2020-08-10T03:16:12 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:17:18 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:17:19 prefetch.2.10.7: 'SRR11471312' is valid 2020-08-10T03:17:19 prefetch.2.10.7: 1) 'SRR11471312' was downloaded successfully Read 13271302 spots for SRR11471312/SRR11471312.sra Written 13271302 spots for SRR11471312/SRR11471312.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:32:34 13271302 reads; of these: 13271302 (100.00%) were unpaired; of these: 1275253 (9.61%) aligned 0 times 5837314 (43.98%) aligned exactly 1 time 6158735 (46.41%) aligned >1 times 90.39% overall alignment rate Time searching: 00:32:36 Overall time: 00:32:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1193507 / 11996049 = 0.0995 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 @ Mon, 10 Aug 2020 12:54:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 12:54:20: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:54:20: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:54:25: 1000000 INFO @ Mon, 10 Aug 2020 12:54:30: 2000000 INFO @ Mon, 10 Aug 2020 12:54:35: 3000000 INFO @ Mon, 10 Aug 2020 12:54:40: 4000000 INFO @ Mon, 10 Aug 2020 12:54:45: 5000000 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 @ Mon, 10 Aug 2020 12:54:50: 6000000 INFO @ Mon, 10 Aug 2020 12:54:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 12:54:50: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:54:50: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:54:55: 7000000 INFO @ Mon, 10 Aug 2020 12:54:55: 1000000 INFO @ Mon, 10 Aug 2020 12:55:00: 8000000 INFO @ Mon, 10 Aug 2020 12:55:00: 2000000 INFO @ Mon, 10 Aug 2020 12:55:05: 9000000 INFO @ Mon, 10 Aug 2020 12:55:05: 3000000 INFO @ Mon, 10 Aug 2020 12:55:10: 10000000 INFO @ Mon, 10 Aug 2020 12:55:10: 4000000 INFO @ Mon, 10 Aug 2020 12:55:14: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:55:14: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:55:14: #1 total tags in treatment: 10802542 INFO @ Mon, 10 Aug 2020 12:55:14: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:55:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:55:15: #1 tags after filtering in treatment: 10802365 INFO @ Mon, 10 Aug 2020 12:55:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:55:15: #1 finished! INFO @ Mon, 10 Aug 2020 12:55:15: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:55:15: 5000000 INFO @ Mon, 10 Aug 2020 12:55:17: #2 number of paired peaks: 25404 INFO @ Mon, 10 Aug 2020 12:55:17: start model_add_line... INFO @ Mon, 10 Aug 2020 12:55:17: start X-correlation... INFO @ Mon, 10 Aug 2020 12:55:17: end of X-cor INFO @ Mon, 10 Aug 2020 12:55:17: #2 finished! INFO @ Mon, 10 Aug 2020 12:55:17: #2 predicted fragment length is 54 bps INFO @ Mon, 10 Aug 2020 12:55:17: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 10 Aug 2020 12:55:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.05_model.r WARNING @ Mon, 10 Aug 2020 12:55:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:55:17: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 10 Aug 2020 12:55:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 12:55:17: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:55:17: #3 Pre-compute pvalue-qvalue table... 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 @ Mon, 10 Aug 2020 12:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Mon, 10 Aug 2020 12:55:20: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:55:20: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:55:20: 6000000 INFO @ Mon, 10 Aug 2020 12:55:25: 7000000 INFO @ Mon, 10 Aug 2020 12:55:26: 1000000 INFO @ Mon, 10 Aug 2020 12:55:30: 8000000 INFO @ Mon, 10 Aug 2020 12:55:31: 2000000 INFO @ Mon, 10 Aug 2020 12:55:36: 9000000 INFO @ Mon, 10 Aug 2020 12:55:37: 3000000 INFO @ Mon, 10 Aug 2020 12:55:40: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:55:41: 10000000 INFO @ Mon, 10 Aug 2020 12:55:43: 4000000 INFO @ Mon, 10 Aug 2020 12:55:45: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:55:45: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:55:45: #1 total tags in treatment: 10802542 INFO @ Mon, 10 Aug 2020 12:55:45: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:55:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:55:45: #1 tags after filtering in treatment: 10802365 INFO @ Mon, 10 Aug 2020 12:55:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:55:45: #1 finished! INFO @ Mon, 10 Aug 2020 12:55:45: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:55:47: #2 number of paired peaks: 25404 INFO @ Mon, 10 Aug 2020 12:55:47: start model_add_line... INFO @ Mon, 10 Aug 2020 12:55:47: start X-correlation... INFO @ Mon, 10 Aug 2020 12:55:47: end of X-cor INFO @ Mon, 10 Aug 2020 12:55:47: #2 finished! INFO @ Mon, 10 Aug 2020 12:55:47: #2 predicted fragment length is 54 bps INFO @ Mon, 10 Aug 2020 12:55:47: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 10 Aug 2020 12:55:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.10_model.r WARNING @ Mon, 10 Aug 2020 12:55:47: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:55:47: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 10 Aug 2020 12:55:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 12:55:47: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:55:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:55:49: 5000000 INFO @ Mon, 10 Aug 2020 12:55:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:55:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:55:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.05_summits.bed INFO @ Mon, 10 Aug 2020 12:55:53: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (5904 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:55:54: 6000000 INFO @ Mon, 10 Aug 2020 12:56:00: 7000000 INFO @ Mon, 10 Aug 2020 12:56:06: 8000000 INFO @ Mon, 10 Aug 2020 12:56:11: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:56:11: 9000000 INFO @ Mon, 10 Aug 2020 12:56:17: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:56:22: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:56:22: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:56:22: #1 total tags in treatment: 10802542 INFO @ Mon, 10 Aug 2020 12:56:22: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:56:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 12:56:22: #1 tags after filtering in treatment: 10802365 INFO @ Mon, 10 Aug 2020 12:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:56:22: #1 finished! INFO @ Mon, 10 Aug 2020 12:56:22: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.10_summits.bed INFO @ Mon, 10 Aug 2020 12:56:23: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (1603 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:56:24: #2 number of paired peaks: 25404 INFO @ Mon, 10 Aug 2020 12:56:24: start model_add_line... INFO @ Mon, 10 Aug 2020 12:56:24: start X-correlation... INFO @ Mon, 10 Aug 2020 12:56:24: end of X-cor INFO @ Mon, 10 Aug 2020 12:56:24: #2 finished! INFO @ Mon, 10 Aug 2020 12:56:24: #2 predicted fragment length is 54 bps INFO @ Mon, 10 Aug 2020 12:56:24: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 10 Aug 2020 12:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.20_model.r WARNING @ Mon, 10 Aug 2020 12:56:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:56:24: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 10 Aug 2020 12:56:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 12:56:24: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:56:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:56:49: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047587/SRX8047587.20_summits.bed INFO @ Mon, 10 Aug 2020 12:57:00: Done! pass1 - making usageList (32 chroms): 0 millis pass2 - checking and writing primary data (554 records, 4 fields): 3 millis CompletedMACS2peakCalling