Job ID = 8184309 SRX = SRX8047586 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:15:57 prefetch.2.10.7: 1) Downloading 'SRR11471311'... 2020-08-10T03:15:57 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:17:11 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:17:11 prefetch.2.10.7: 1) 'SRR11471311' was downloaded successfully Read 18824075 spots for SRR11471311/SRR11471311.sra Written 18824075 spots for SRR11471311/SRR11471311.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:51:25 18824075 reads; of these: 18824075 (100.00%) were unpaired; of these: 1196014 (6.35%) aligned 0 times 8850565 (47.02%) aligned exactly 1 time 8777496 (46.63%) aligned >1 times 93.65% overall alignment rate Time searching: 00:51:28 Overall time: 00:51:28 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] 2659590 / 17628061 = 0.1509 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 13:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.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 13:14:42: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:14:42: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:14:49: 1000000 INFO @ Mon, 10 Aug 2020 13:14:56: 2000000 INFO @ Mon, 10 Aug 2020 13:15:02: 3000000 INFO @ Mon, 10 Aug 2020 13:15:09: 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 @ Mon, 10 Aug 2020 13:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.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 13:15:12: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:15:12: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:15:16: 5000000 INFO @ Mon, 10 Aug 2020 13:15:19: 1000000 INFO @ Mon, 10 Aug 2020 13:15:23: 6000000 INFO @ Mon, 10 Aug 2020 13:15:26: 2000000 INFO @ Mon, 10 Aug 2020 13:15:30: 7000000 INFO @ Mon, 10 Aug 2020 13:15:32: 3000000 INFO @ Mon, 10 Aug 2020 13:15:37: 8000000 INFO @ Mon, 10 Aug 2020 13:15:39: 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 @ Mon, 10 Aug 2020 13:15:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.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 13:15:43: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:15:43: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:15:44: 9000000 INFO @ Mon, 10 Aug 2020 13:15:45: 5000000 INFO @ Mon, 10 Aug 2020 13:15:49: 1000000 INFO @ Mon, 10 Aug 2020 13:15:51: 10000000 INFO @ Mon, 10 Aug 2020 13:15:52: 6000000 INFO @ Mon, 10 Aug 2020 13:15:56: 2000000 INFO @ Mon, 10 Aug 2020 13:15:59: 11000000 INFO @ Mon, 10 Aug 2020 13:15:59: 7000000 INFO @ Mon, 10 Aug 2020 13:16:03: 3000000 INFO @ Mon, 10 Aug 2020 13:16:06: 8000000 INFO @ Mon, 10 Aug 2020 13:16:06: 12000000 INFO @ Mon, 10 Aug 2020 13:16:10: 4000000 INFO @ Mon, 10 Aug 2020 13:16:12: 9000000 INFO @ Mon, 10 Aug 2020 13:16:14: 13000000 INFO @ Mon, 10 Aug 2020 13:16:16: 5000000 INFO @ Mon, 10 Aug 2020 13:16:19: 10000000 INFO @ Mon, 10 Aug 2020 13:16:21: 14000000 INFO @ Mon, 10 Aug 2020 13:16:23: 6000000 INFO @ Mon, 10 Aug 2020 13:16:26: 11000000 INFO @ Mon, 10 Aug 2020 13:16:29: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:16:29: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:16:29: #1 total tags in treatment: 14968471 INFO @ Mon, 10 Aug 2020 13:16:29: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:16:29: #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 13:16:29: #1 tags after filtering in treatment: 14968329 INFO @ Mon, 10 Aug 2020 13:16:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:16:29: #1 finished! INFO @ Mon, 10 Aug 2020 13:16:29: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:16:30: 7000000 INFO @ Mon, 10 Aug 2020 13:16:32: #2 number of paired peaks: 35041 INFO @ Mon, 10 Aug 2020 13:16:32: start model_add_line... INFO @ Mon, 10 Aug 2020 13:16:32: start X-correlation... INFO @ Mon, 10 Aug 2020 13:16:32: end of X-cor INFO @ Mon, 10 Aug 2020 13:16:32: #2 finished! INFO @ Mon, 10 Aug 2020 13:16:32: #2 predicted fragment length is 57 bps INFO @ Mon, 10 Aug 2020 13:16:32: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 10 Aug 2020 13:16:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.05_model.r WARNING @ Mon, 10 Aug 2020 13:16:32: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:16:32: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 10 Aug 2020 13:16:32: #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 13:16:32: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:16:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:16:33: 12000000 INFO @ Mon, 10 Aug 2020 13:16:37: 8000000 INFO @ Mon, 10 Aug 2020 13:16:39: 13000000 INFO @ Mon, 10 Aug 2020 13:16:43: 9000000 INFO @ Mon, 10 Aug 2020 13:16:46: 14000000 INFO @ Mon, 10 Aug 2020 13:16:50: 10000000 INFO @ Mon, 10 Aug 2020 13:16:52: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:16:52: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:16:52: #1 total tags in treatment: 14968471 INFO @ Mon, 10 Aug 2020 13:16:52: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:16:52: #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 13:16:52: #1 tags after filtering in treatment: 14968329 INFO @ Mon, 10 Aug 2020 13:16:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:16:52: #1 finished! INFO @ Mon, 10 Aug 2020 13:16:52: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:16:55: #2 number of paired peaks: 35041 INFO @ Mon, 10 Aug 2020 13:16:55: start model_add_line... INFO @ Mon, 10 Aug 2020 13:16:55: start X-correlation... INFO @ Mon, 10 Aug 2020 13:16:55: end of X-cor INFO @ Mon, 10 Aug 2020 13:16:55: #2 finished! INFO @ Mon, 10 Aug 2020 13:16:55: #2 predicted fragment length is 57 bps INFO @ Mon, 10 Aug 2020 13:16:55: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 10 Aug 2020 13:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.10_model.r WARNING @ Mon, 10 Aug 2020 13:16:55: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:16:55: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 10 Aug 2020 13:16:55: #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 13:16:55: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:16:56: 11000000 INFO @ Mon, 10 Aug 2020 13:17:02: 12000000 INFO @ Mon, 10 Aug 2020 13:17:07: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:17:08: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:17:14: 14000000 INFO @ Mon, 10 Aug 2020 13:17:20: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:17:20: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:17:20: #1 total tags in treatment: 14968471 INFO @ Mon, 10 Aug 2020 13:17:20: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:17:20: #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 13:17:20: #1 tags after filtering in treatment: 14968329 INFO @ Mon, 10 Aug 2020 13:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:17:20: #1 finished! INFO @ Mon, 10 Aug 2020 13:17:20: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:17:23: #2 number of paired peaks: 35041 INFO @ Mon, 10 Aug 2020 13:17:23: start model_add_line... INFO @ Mon, 10 Aug 2020 13:17:23: start X-correlation... INFO @ Mon, 10 Aug 2020 13:17:23: end of X-cor INFO @ Mon, 10 Aug 2020 13:17:23: #2 finished! INFO @ Mon, 10 Aug 2020 13:17:23: #2 predicted fragment length is 57 bps INFO @ Mon, 10 Aug 2020 13:17:23: #2 alternative fragment length(s) may be 57 bps INFO @ Mon, 10 Aug 2020 13:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.20_model.r WARNING @ Mon, 10 Aug 2020 13:17:23: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:17:23: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Mon, 10 Aug 2020 13:17:23: #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 13:17:23: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.05_summits.bed INFO @ Mon, 10 Aug 2020 13:17:25: Done! pass1 - making usageList (99 chroms): 3 millis pass2 - checking and writing primary data (12976 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:17:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:17:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:17:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:17:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.10_summits.bed INFO @ Mon, 10 Aug 2020 13:17:47: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (3608 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:17:58: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047586/SRX8047586.20_summits.bed INFO @ Mon, 10 Aug 2020 13:18:17: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (940 records, 4 fields): 4 millis CompletedMACS2peakCalling