Job ID = 5790785 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,805,269 reads read : 83,610,538 reads written : 41,805,269 reads 0-length : 41,805,269 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: 00:00:01 Multiseed full-index search: 00:39:18 41805269 reads; of these: 41805269 (100.00%) were unpaired; of these: 3983397 (9.53%) aligned 0 times 26391877 (63.13%) aligned exactly 1 time 11429995 (27.34%) aligned >1 times 90.47% overall alignment rate Time searching: 00:39:21 Overall time: 00:39:21 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 16 files... [bam_rmdupse_core] 11355196 / 37821872 = 0.3002 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 08:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.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 08:17:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:17:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:33: 1000000 INFO @ Wed, 22 Apr 2020 08:17:40: 2000000 INFO @ Wed, 22 Apr 2020 08:17:48: 3000000 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 08:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.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 08:17:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:17:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:55: 4000000 INFO @ Wed, 22 Apr 2020 08:18:03: 5000000 INFO @ Wed, 22 Apr 2020 08:18:03: 1000000 INFO @ Wed, 22 Apr 2020 08:18:10: 6000000 INFO @ Wed, 22 Apr 2020 08:18:11: 2000000 INFO @ Wed, 22 Apr 2020 08:18:18: 7000000 INFO @ Wed, 22 Apr 2020 08:18:19: 3000000 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 08:18:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.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 08:18:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:18:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:18:25: 8000000 INFO @ Wed, 22 Apr 2020 08:18:26: 4000000 INFO @ Wed, 22 Apr 2020 08:18:32: 1000000 INFO @ Wed, 22 Apr 2020 08:18:33: 9000000 INFO @ Wed, 22 Apr 2020 08:18:34: 5000000 INFO @ Wed, 22 Apr 2020 08:18:39: 2000000 INFO @ Wed, 22 Apr 2020 08:18:41: 10000000 INFO @ Wed, 22 Apr 2020 08:18:42: 6000000 INFO @ Wed, 22 Apr 2020 08:18:45: 3000000 INFO @ Wed, 22 Apr 2020 08:18:48: 11000000 INFO @ Wed, 22 Apr 2020 08:18:50: 7000000 INFO @ Wed, 22 Apr 2020 08:18:52: 4000000 INFO @ Wed, 22 Apr 2020 08:18:56: 12000000 INFO @ Wed, 22 Apr 2020 08:18:57: 8000000 INFO @ Wed, 22 Apr 2020 08:18:59: 5000000 INFO @ Wed, 22 Apr 2020 08:19:03: 13000000 INFO @ Wed, 22 Apr 2020 08:19:05: 9000000 INFO @ Wed, 22 Apr 2020 08:19:06: 6000000 INFO @ Wed, 22 Apr 2020 08:19:11: 14000000 INFO @ Wed, 22 Apr 2020 08:19:12: 10000000 INFO @ Wed, 22 Apr 2020 08:19:13: 7000000 INFO @ Wed, 22 Apr 2020 08:19:18: 15000000 INFO @ Wed, 22 Apr 2020 08:19:20: 11000000 INFO @ Wed, 22 Apr 2020 08:19:20: 8000000 INFO @ Wed, 22 Apr 2020 08:19:26: 16000000 INFO @ Wed, 22 Apr 2020 08:19:27: 9000000 INFO @ Wed, 22 Apr 2020 08:19:28: 12000000 INFO @ Wed, 22 Apr 2020 08:19:34: 17000000 INFO @ Wed, 22 Apr 2020 08:19:34: 10000000 INFO @ Wed, 22 Apr 2020 08:19:35: 13000000 INFO @ Wed, 22 Apr 2020 08:19:41: 18000000 INFO @ Wed, 22 Apr 2020 08:19:41: 11000000 INFO @ Wed, 22 Apr 2020 08:19:43: 14000000 INFO @ Wed, 22 Apr 2020 08:19:48: 12000000 INFO @ Wed, 22 Apr 2020 08:19:49: 19000000 INFO @ Wed, 22 Apr 2020 08:19:51: 15000000 INFO @ Wed, 22 Apr 2020 08:19:55: 13000000 INFO @ Wed, 22 Apr 2020 08:19:57: 20000000 INFO @ Wed, 22 Apr 2020 08:19:59: 16000000 INFO @ Wed, 22 Apr 2020 08:20:03: 14000000 INFO @ Wed, 22 Apr 2020 08:20:04: 21000000 INFO @ Wed, 22 Apr 2020 08:20:06: 17000000 INFO @ Wed, 22 Apr 2020 08:20:10: 15000000 INFO @ Wed, 22 Apr 2020 08:20:12: 22000000 INFO @ Wed, 22 Apr 2020 08:20:14: 18000000 INFO @ Wed, 22 Apr 2020 08:20:17: 16000000 INFO @ Wed, 22 Apr 2020 08:20:19: 23000000 INFO @ Wed, 22 Apr 2020 08:20:22: 19000000 INFO @ Wed, 22 Apr 2020 08:20:24: 17000000 INFO @ Wed, 22 Apr 2020 08:20:27: 24000000 INFO @ Wed, 22 Apr 2020 08:20:30: 20000000 INFO @ Wed, 22 Apr 2020 08:20:30: 18000000 INFO @ Wed, 22 Apr 2020 08:20:35: 25000000 INFO @ Wed, 22 Apr 2020 08:20:37: 19000000 INFO @ Wed, 22 Apr 2020 08:20:38: 21000000 INFO @ Wed, 22 Apr 2020 08:20:43: 26000000 INFO @ Wed, 22 Apr 2020 08:20:44: 20000000 INFO @ Wed, 22 Apr 2020 08:20:46: 22000000 INFO @ Wed, 22 Apr 2020 08:20:47: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 08:20:47: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 08:20:47: #1 total tags in treatment: 26466676 INFO @ Wed, 22 Apr 2020 08:20:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:20:47: #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 08:20:47: #1 tags after filtering in treatment: 26466570 INFO @ Wed, 22 Apr 2020 08:20:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:20:47: #1 finished! INFO @ Wed, 22 Apr 2020 08:20:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:20:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:20:50: #2 number of paired peaks: 5466 INFO @ Wed, 22 Apr 2020 08:20:50: start model_add_line... INFO @ Wed, 22 Apr 2020 08:20:50: start X-correlation... INFO @ Wed, 22 Apr 2020 08:20:50: end of X-cor INFO @ Wed, 22 Apr 2020 08:20:50: #2 finished! INFO @ Wed, 22 Apr 2020 08:20:50: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 08:20:50: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 08:20:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.05_model.r WARNING @ Wed, 22 Apr 2020 08:20:50: #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 08:20:50: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 08:20:50: #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 08:20:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:20:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:20:51: 21000000 INFO @ Wed, 22 Apr 2020 08:20:54: 23000000 INFO @ Wed, 22 Apr 2020 08:20:58: 22000000 INFO @ Wed, 22 Apr 2020 08:21:02: 24000000 INFO @ Wed, 22 Apr 2020 08:21:04: 23000000 INFO @ Wed, 22 Apr 2020 08:21:10: 25000000 INFO @ Wed, 22 Apr 2020 08:21:11: 24000000 INFO @ Wed, 22 Apr 2020 08:21:18: 26000000 INFO @ Wed, 22 Apr 2020 08:21:18: 25000000 INFO @ Wed, 22 Apr 2020 08:21:22: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 08:21:22: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 08:21:22: #1 total tags in treatment: 26466676 INFO @ Wed, 22 Apr 2020 08:21:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:21:22: #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 08:21:22: #1 tags after filtering in treatment: 26466570 INFO @ Wed, 22 Apr 2020 08:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:21:22: #1 finished! INFO @ Wed, 22 Apr 2020 08:21:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:21:25: 26000000 INFO @ Wed, 22 Apr 2020 08:21:25: #2 number of paired peaks: 5466 INFO @ Wed, 22 Apr 2020 08:21:25: start model_add_line... INFO @ Wed, 22 Apr 2020 08:21:25: start X-correlation... INFO @ Wed, 22 Apr 2020 08:21:25: end of X-cor INFO @ Wed, 22 Apr 2020 08:21:25: #2 finished! INFO @ Wed, 22 Apr 2020 08:21:25: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 08:21:25: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 08:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.10_model.r WARNING @ Wed, 22 Apr 2020 08:21:25: #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 08:21:25: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 08:21:25: #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 08:21:25: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:21:28: #1 tag size is determined as 73 bps INFO @ Wed, 22 Apr 2020 08:21:28: #1 tag size = 73 INFO @ Wed, 22 Apr 2020 08:21:28: #1 total tags in treatment: 26466676 INFO @ Wed, 22 Apr 2020 08:21:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:21:28: #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 08:21:29: #1 tags after filtering in treatment: 26466570 INFO @ Wed, 22 Apr 2020 08:21:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:21:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:21:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:21:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:21:31: #2 number of paired peaks: 5466 INFO @ Wed, 22 Apr 2020 08:21:31: start model_add_line... INFO @ Wed, 22 Apr 2020 08:21:31: start X-correlation... INFO @ Wed, 22 Apr 2020 08:21:31: end of X-cor INFO @ Wed, 22 Apr 2020 08:21:31: #2 finished! INFO @ Wed, 22 Apr 2020 08:21:31: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 08:21:31: #2 alternative fragment length(s) may be 74 bps INFO @ Wed, 22 Apr 2020 08:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.20_model.r WARNING @ Wed, 22 Apr 2020 08:21:31: #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 08:21:31: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Wed, 22 Apr 2020 08:21:31: #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 08:21:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:21:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:22:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:22:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.05_summits.bed INFO @ Wed, 22 Apr 2020 08:22:30: Done! INFO @ Wed, 22 Apr 2020 08:22:30: #3 Call peaks for each chromosome... pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (1500 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:22:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:23:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:23:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:23:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.10_summits.bed INFO @ Wed, 22 Apr 2020 08:23:05: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:23:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:23:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:23:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625155/SRX7625155.20_summits.bed INFO @ Wed, 22 Apr 2020 08:23:12: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。