Job ID = 5790777 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,446,416 reads read : 44,892,832 reads written : 22,446,416 reads 0-length : 22,446,416 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:15:34 22446416 reads; of these: 22446416 (100.00%) were unpaired; of these: 656098 (2.92%) aligned 0 times 16068299 (71.59%) aligned exactly 1 time 5722019 (25.49%) aligned >1 times 97.08% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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 12 files... [bam_rmdupse_core] 4970686 / 21790318 = 0.2281 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 @ Wed, 22 Apr 2020 07:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.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 @ Wed, 22 Apr 2020 07:24:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:24:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:25:01: 1000000 INFO @ Wed, 22 Apr 2020 07:25:07: 2000000 INFO @ Wed, 22 Apr 2020 07:25:13: 3000000 INFO @ Wed, 22 Apr 2020 07:25:20: 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 @ Wed, 22 Apr 2020 07:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.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 @ Wed, 22 Apr 2020 07:25:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:25:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:25:26: 5000000 INFO @ Wed, 22 Apr 2020 07:25:32: 1000000 INFO @ Wed, 22 Apr 2020 07:25:34: 6000000 INFO @ Wed, 22 Apr 2020 07:25:39: 2000000 INFO @ Wed, 22 Apr 2020 07:25:41: 7000000 INFO @ Wed, 22 Apr 2020 07:25:47: 3000000 INFO @ Wed, 22 Apr 2020 07:25:48: 8000000 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 @ Wed, 22 Apr 2020 07:25:54: 4000000 INFO @ Wed, 22 Apr 2020 07:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.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 @ Wed, 22 Apr 2020 07:25:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:25:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:25:56: 9000000 INFO @ Wed, 22 Apr 2020 07:26:02: 5000000 INFO @ Wed, 22 Apr 2020 07:26:02: 1000000 INFO @ Wed, 22 Apr 2020 07:26:03: 10000000 INFO @ Wed, 22 Apr 2020 07:26:09: 6000000 INFO @ Wed, 22 Apr 2020 07:26:09: 2000000 INFO @ Wed, 22 Apr 2020 07:26:11: 11000000 INFO @ Wed, 22 Apr 2020 07:26:17: 7000000 INFO @ Wed, 22 Apr 2020 07:26:17: 3000000 INFO @ Wed, 22 Apr 2020 07:26:18: 12000000 INFO @ Wed, 22 Apr 2020 07:26:24: 8000000 INFO @ Wed, 22 Apr 2020 07:26:25: 4000000 INFO @ Wed, 22 Apr 2020 07:26:26: 13000000 INFO @ Wed, 22 Apr 2020 07:26:32: 9000000 INFO @ Wed, 22 Apr 2020 07:26:32: 5000000 INFO @ Wed, 22 Apr 2020 07:26:33: 14000000 INFO @ Wed, 22 Apr 2020 07:26:40: 10000000 INFO @ Wed, 22 Apr 2020 07:26:40: 6000000 INFO @ Wed, 22 Apr 2020 07:26:41: 15000000 INFO @ Wed, 22 Apr 2020 07:26:47: 11000000 INFO @ Wed, 22 Apr 2020 07:26:47: 7000000 INFO @ Wed, 22 Apr 2020 07:26:48: 16000000 INFO @ Wed, 22 Apr 2020 07:26:55: 12000000 INFO @ Wed, 22 Apr 2020 07:26:55: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:26:55: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:26:55: #1 total tags in treatment: 16819632 INFO @ Wed, 22 Apr 2020 07:26:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:26:55: 8000000 INFO @ Wed, 22 Apr 2020 07:26:55: #1 tags after filtering in treatment: 16819471 INFO @ Wed, 22 Apr 2020 07:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:26:55: #1 finished! INFO @ Wed, 22 Apr 2020 07:26:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:26:57: #2 number of paired peaks: 3684 INFO @ Wed, 22 Apr 2020 07:26:57: start model_add_line... INFO @ Wed, 22 Apr 2020 07:26:57: start X-correlation... INFO @ Wed, 22 Apr 2020 07:26:57: end of X-cor INFO @ Wed, 22 Apr 2020 07:26:57: #2 finished! INFO @ Wed, 22 Apr 2020 07:26:57: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:26:57: #2 alternative fragment length(s) may be 74,566 bps INFO @ Wed, 22 Apr 2020 07:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.05_model.r WARNING @ Wed, 22 Apr 2020 07:26:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:26:57: #2 You may need to consider one of the other alternative d(s): 74,566 WARNING @ Wed, 22 Apr 2020 07:26:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:26:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:27:02: 13000000 INFO @ Wed, 22 Apr 2020 07:27:02: 9000000 INFO @ Wed, 22 Apr 2020 07:27:10: 14000000 INFO @ Wed, 22 Apr 2020 07:27:10: 10000000 INFO @ Wed, 22 Apr 2020 07:27:17: 15000000 INFO @ Wed, 22 Apr 2020 07:27:17: 11000000 INFO @ Wed, 22 Apr 2020 07:27:25: 16000000 INFO @ Wed, 22 Apr 2020 07:27:25: 12000000 INFO @ Wed, 22 Apr 2020 07:27:31: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:27:31: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:27:31: #1 total tags in treatment: 16819632 INFO @ Wed, 22 Apr 2020 07:27:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:27:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:27:32: #1 tags after filtering in treatment: 16819471 INFO @ Wed, 22 Apr 2020 07:27:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:27:32: #1 finished! INFO @ Wed, 22 Apr 2020 07:27:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:27:32: 13000000 INFO @ Wed, 22 Apr 2020 07:27:33: #2 number of paired peaks: 3684 INFO @ Wed, 22 Apr 2020 07:27:33: start model_add_line... INFO @ Wed, 22 Apr 2020 07:27:33: start X-correlation... INFO @ Wed, 22 Apr 2020 07:27:33: end of X-cor INFO @ Wed, 22 Apr 2020 07:27:33: #2 finished! INFO @ Wed, 22 Apr 2020 07:27:33: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:27:33: #2 alternative fragment length(s) may be 74,566 bps INFO @ Wed, 22 Apr 2020 07:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.10_model.r WARNING @ Wed, 22 Apr 2020 07:27:33: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:27:33: #2 You may need to consider one of the other alternative d(s): 74,566 WARNING @ Wed, 22 Apr 2020 07:27:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:27:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:27:35: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:27:39: 14000000 INFO @ Wed, 22 Apr 2020 07:27:46: 15000000 INFO @ Wed, 22 Apr 2020 07:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.05_summits.bed INFO @ Wed, 22 Apr 2020 07:27:52: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (851 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:27:53: 16000000 INFO @ Wed, 22 Apr 2020 07:27:58: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:27:58: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:27:58: #1 total tags in treatment: 16819632 INFO @ Wed, 22 Apr 2020 07:27:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:27:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:27:59: #1 tags after filtering in treatment: 16819471 INFO @ Wed, 22 Apr 2020 07:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:27:59: #1 finished! INFO @ Wed, 22 Apr 2020 07:27:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:28:00: #2 number of paired peaks: 3684 INFO @ Wed, 22 Apr 2020 07:28:00: start model_add_line... INFO @ Wed, 22 Apr 2020 07:28:00: start X-correlation... INFO @ Wed, 22 Apr 2020 07:28:00: end of X-cor INFO @ Wed, 22 Apr 2020 07:28:00: #2 finished! INFO @ Wed, 22 Apr 2020 07:28:00: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:28:00: #2 alternative fragment length(s) may be 74,566 bps INFO @ Wed, 22 Apr 2020 07:28:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.20_model.r WARNING @ Wed, 22 Apr 2020 07:28:00: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:28:00: #2 You may need to consider one of the other alternative d(s): 74,566 WARNING @ Wed, 22 Apr 2020 07:28:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:28:00: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:28:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:28:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.10_summits.bed INFO @ Wed, 22 Apr 2020 07:28:29: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:28:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625151/SRX7625151.20_summits.bed INFO @ Wed, 22 Apr 2020 07:28:56: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。