Job ID = 5790636 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 50,051,928 reads read : 100,103,856 reads written : 50,051,928 reads 0-length : 50,051,928 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: 00:00:03 Multiseed full-index search: 00:37:46 50051928 reads; of these: 50051928 (100.00%) were unpaired; of these: 5186025 (10.36%) aligned 0 times 41079717 (82.07%) aligned exactly 1 time 3786186 (7.56%) aligned >1 times 89.64% overall alignment rate Time searching: 00:37:50 Overall time: 00:37:50 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 20 files... [bam_rmdupse_core] 23225843 / 44865903 = 0.5177 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 05:46:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.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 05:46:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:46:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:46:17: 1000000 INFO @ Wed, 22 Apr 2020 05:46:23: 2000000 INFO @ Wed, 22 Apr 2020 05:46:30: 3000000 INFO @ Wed, 22 Apr 2020 05:46:37: 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 @ Wed, 22 Apr 2020 05:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.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 05:46:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:46:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:46:44: 5000000 INFO @ Wed, 22 Apr 2020 05:46:45: 1000000 INFO @ Wed, 22 Apr 2020 05:46:51: 2000000 INFO @ Wed, 22 Apr 2020 05:46:51: 6000000 INFO @ Wed, 22 Apr 2020 05:46:57: 3000000 INFO @ Wed, 22 Apr 2020 05:46:58: 7000000 INFO @ Wed, 22 Apr 2020 05:47:02: 4000000 INFO @ Wed, 22 Apr 2020 05:47:05: 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 05:47:08: 5000000 INFO @ Wed, 22 Apr 2020 05:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.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 05:47:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:47:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:47:12: 9000000 INFO @ Wed, 22 Apr 2020 05:47:14: 6000000 INFO @ Wed, 22 Apr 2020 05:47:16: 1000000 INFO @ Wed, 22 Apr 2020 05:47:19: 10000000 INFO @ Wed, 22 Apr 2020 05:47:20: 7000000 INFO @ Wed, 22 Apr 2020 05:47:22: 2000000 INFO @ Wed, 22 Apr 2020 05:47:26: 8000000 INFO @ Wed, 22 Apr 2020 05:47:26: 11000000 INFO @ Wed, 22 Apr 2020 05:47:28: 3000000 INFO @ Wed, 22 Apr 2020 05:47:32: 9000000 INFO @ Wed, 22 Apr 2020 05:47:33: 12000000 INFO @ Wed, 22 Apr 2020 05:47:34: 4000000 INFO @ Wed, 22 Apr 2020 05:47:37: 10000000 INFO @ Wed, 22 Apr 2020 05:47:40: 13000000 INFO @ Wed, 22 Apr 2020 05:47:40: 5000000 INFO @ Wed, 22 Apr 2020 05:47:43: 11000000 INFO @ Wed, 22 Apr 2020 05:47:46: 6000000 INFO @ Wed, 22 Apr 2020 05:47:47: 14000000 INFO @ Wed, 22 Apr 2020 05:47:49: 12000000 INFO @ Wed, 22 Apr 2020 05:47:52: 7000000 INFO @ Wed, 22 Apr 2020 05:47:54: 15000000 INFO @ Wed, 22 Apr 2020 05:47:55: 13000000 INFO @ Wed, 22 Apr 2020 05:47:58: 8000000 INFO @ Wed, 22 Apr 2020 05:48:01: 16000000 INFO @ Wed, 22 Apr 2020 05:48:01: 14000000 INFO @ Wed, 22 Apr 2020 05:48:03: 9000000 INFO @ Wed, 22 Apr 2020 05:48:07: 15000000 INFO @ Wed, 22 Apr 2020 05:48:08: 17000000 INFO @ Wed, 22 Apr 2020 05:48:09: 10000000 INFO @ Wed, 22 Apr 2020 05:48:13: 16000000 INFO @ Wed, 22 Apr 2020 05:48:15: 18000000 INFO @ Wed, 22 Apr 2020 05:48:15: 11000000 INFO @ Wed, 22 Apr 2020 05:48:19: 17000000 INFO @ Wed, 22 Apr 2020 05:48:21: 12000000 INFO @ Wed, 22 Apr 2020 05:48:22: 19000000 INFO @ Wed, 22 Apr 2020 05:48:25: 18000000 INFO @ Wed, 22 Apr 2020 05:48:27: 13000000 INFO @ Wed, 22 Apr 2020 05:48:29: 20000000 INFO @ Wed, 22 Apr 2020 05:48:30: 19000000 INFO @ Wed, 22 Apr 2020 05:48:33: 14000000 INFO @ Wed, 22 Apr 2020 05:48:36: 21000000 INFO @ Wed, 22 Apr 2020 05:48:36: 20000000 INFO @ Wed, 22 Apr 2020 05:48:39: 15000000 INFO @ Wed, 22 Apr 2020 05:48:41: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:48:41: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:48:41: #1 total tags in treatment: 21640060 INFO @ Wed, 22 Apr 2020 05:48:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:48:41: #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 05:48:41: #1 tags after filtering in treatment: 21639834 INFO @ Wed, 22 Apr 2020 05:48:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:48:41: #1 finished! INFO @ Wed, 22 Apr 2020 05:48:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:48:42: 21000000 INFO @ Wed, 22 Apr 2020 05:48:43: #2 number of paired peaks: 20831 INFO @ Wed, 22 Apr 2020 05:48:43: start model_add_line... INFO @ Wed, 22 Apr 2020 05:48:44: start X-correlation... INFO @ Wed, 22 Apr 2020 05:48:44: end of X-cor INFO @ Wed, 22 Apr 2020 05:48:44: #2 finished! INFO @ Wed, 22 Apr 2020 05:48:44: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 05:48:44: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 05:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.05_model.r WARNING @ Wed, 22 Apr 2020 05:48:44: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:48:44: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Wed, 22 Apr 2020 05:48:44: #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 05:48:44: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:48:45: 16000000 INFO @ Wed, 22 Apr 2020 05:48:46: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:48:46: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:48:46: #1 total tags in treatment: 21640060 INFO @ Wed, 22 Apr 2020 05:48:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:48:46: #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 05:48:47: #1 tags after filtering in treatment: 21639834 INFO @ Wed, 22 Apr 2020 05:48:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:48:47: #1 finished! INFO @ Wed, 22 Apr 2020 05:48:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:48:49: #2 number of paired peaks: 20831 INFO @ Wed, 22 Apr 2020 05:48:49: start model_add_line... INFO @ Wed, 22 Apr 2020 05:48:49: start X-correlation... INFO @ Wed, 22 Apr 2020 05:48:49: end of X-cor INFO @ Wed, 22 Apr 2020 05:48:49: #2 finished! INFO @ Wed, 22 Apr 2020 05:48:49: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 05:48:49: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 05:48:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.10_model.r WARNING @ Wed, 22 Apr 2020 05:48:49: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:48:49: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Wed, 22 Apr 2020 05:48:49: #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 05:48:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:48:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:48:50: 17000000 INFO @ Wed, 22 Apr 2020 05:48:56: 18000000 INFO @ Wed, 22 Apr 2020 05:49:01: 19000000 INFO @ Wed, 22 Apr 2020 05:49:07: 20000000 INFO @ Wed, 22 Apr 2020 05:49:12: 21000000 INFO @ Wed, 22 Apr 2020 05:49:16: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:49:16: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:49:16: #1 total tags in treatment: 21640060 INFO @ Wed, 22 Apr 2020 05:49:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:49:16: #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 05:49:16: #1 tags after filtering in treatment: 21639834 INFO @ Wed, 22 Apr 2020 05:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:49:16: #1 finished! INFO @ Wed, 22 Apr 2020 05:49:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:49:19: #2 number of paired peaks: 20831 INFO @ Wed, 22 Apr 2020 05:49:19: start model_add_line... INFO @ Wed, 22 Apr 2020 05:49:19: start X-correlation... INFO @ Wed, 22 Apr 2020 05:49:19: end of X-cor INFO @ Wed, 22 Apr 2020 05:49:19: #2 finished! INFO @ Wed, 22 Apr 2020 05:49:19: #2 predicted fragment length is 173 bps INFO @ Wed, 22 Apr 2020 05:49:19: #2 alternative fragment length(s) may be 173 bps INFO @ Wed, 22 Apr 2020 05:49:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.20_model.r WARNING @ Wed, 22 Apr 2020 05:49:19: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:49:19: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Wed, 22 Apr 2020 05:49:19: #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 05:49:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:49:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:49:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.05_summits.bed INFO @ Wed, 22 Apr 2020 05:49:51: Done! pass1 - making usageList (127 chroms): 4 millis pass2 - checking and writing primary data (24615 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.10_summits.bed INFO @ Wed, 22 Apr 2020 05:50:01: Done! pass1 - making usageList (115 chroms): 3 millis pass2 - checking and writing primary data (21935 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:50:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299280/SRX5299280.20_summits.bed INFO @ Wed, 22 Apr 2020 05:50:29: Done! pass1 - making usageList (104 chroms): 3 millis pass2 - checking and writing primary data (19726 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。