Job ID = 5790707 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,992,676 reads read : 36,992,676 reads written : 36,992,676 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8982440.sra.cache’: 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: 00:13:00 36992676 reads; of these: 36992676 (100.00%) were unpaired; of these: 7742223 (20.93%) aligned 0 times 19439514 (52.55%) aligned exactly 1 time 9810939 (26.52%) aligned >1 times 79.07% overall alignment rate Time searching: 00:13:01 Overall time: 00:13:01 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] 5169021 / 29250453 = 0.1767 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 06:41:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.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 06:41:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:41:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:41:38: 1000000 INFO @ Wed, 22 Apr 2020 06:41:45: 2000000 INFO @ Wed, 22 Apr 2020 06:41:51: 3000000 INFO @ Wed, 22 Apr 2020 06:41:58: 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 06:42:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.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 06:42:03: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:42:03: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:42:04: 5000000 INFO @ Wed, 22 Apr 2020 06:42:07: 1000000 INFO @ Wed, 22 Apr 2020 06:42:11: 6000000 INFO @ Wed, 22 Apr 2020 06:42:12: 2000000 INFO @ Wed, 22 Apr 2020 06:42:17: 3000000 INFO @ Wed, 22 Apr 2020 06:42:17: 7000000 INFO @ Wed, 22 Apr 2020 06:42:21: 4000000 INFO @ Wed, 22 Apr 2020 06:42:23: 8000000 INFO @ Wed, 22 Apr 2020 06:42:26: 5000000 INFO @ Wed, 22 Apr 2020 06:42:30: 9000000 INFO @ Wed, 22 Apr 2020 06:42:31: 6000000 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 06:42:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.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 06:42:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:42:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:42:35: 7000000 INFO @ Wed, 22 Apr 2020 06:42:36: 10000000 INFO @ Wed, 22 Apr 2020 06:42:38: 1000000 INFO @ Wed, 22 Apr 2020 06:42:40: 8000000 INFO @ Wed, 22 Apr 2020 06:42:43: 11000000 INFO @ Wed, 22 Apr 2020 06:42:44: 2000000 INFO @ Wed, 22 Apr 2020 06:42:45: 9000000 INFO @ Wed, 22 Apr 2020 06:42:49: 3000000 INFO @ Wed, 22 Apr 2020 06:42:50: 10000000 INFO @ Wed, 22 Apr 2020 06:42:50: 12000000 INFO @ Wed, 22 Apr 2020 06:42:54: 11000000 INFO @ Wed, 22 Apr 2020 06:42:55: 4000000 INFO @ Wed, 22 Apr 2020 06:42:58: 13000000 INFO @ Wed, 22 Apr 2020 06:42:59: 12000000 INFO @ Wed, 22 Apr 2020 06:43:01: 5000000 INFO @ Wed, 22 Apr 2020 06:43:04: 13000000 INFO @ Wed, 22 Apr 2020 06:43:05: 14000000 INFO @ Wed, 22 Apr 2020 06:43:07: 6000000 INFO @ Wed, 22 Apr 2020 06:43:08: 14000000 INFO @ Wed, 22 Apr 2020 06:43:12: 7000000 INFO @ Wed, 22 Apr 2020 06:43:13: 15000000 INFO @ Wed, 22 Apr 2020 06:43:13: 15000000 INFO @ Wed, 22 Apr 2020 06:43:18: 8000000 INFO @ Wed, 22 Apr 2020 06:43:18: 16000000 INFO @ Wed, 22 Apr 2020 06:43:21: 16000000 INFO @ Wed, 22 Apr 2020 06:43:23: 17000000 INFO @ Wed, 22 Apr 2020 06:43:24: 9000000 INFO @ Wed, 22 Apr 2020 06:43:28: 18000000 INFO @ Wed, 22 Apr 2020 06:43:29: 17000000 INFO @ Wed, 22 Apr 2020 06:43:29: 10000000 INFO @ Wed, 22 Apr 2020 06:43:32: 19000000 INFO @ Wed, 22 Apr 2020 06:43:35: 11000000 INFO @ Wed, 22 Apr 2020 06:43:36: 18000000 INFO @ Wed, 22 Apr 2020 06:43:37: 20000000 INFO @ Wed, 22 Apr 2020 06:43:41: 12000000 INFO @ Wed, 22 Apr 2020 06:43:42: 21000000 INFO @ Wed, 22 Apr 2020 06:43:42: 19000000 INFO @ Wed, 22 Apr 2020 06:43:46: 13000000 INFO @ Wed, 22 Apr 2020 06:43:46: 22000000 INFO @ Wed, 22 Apr 2020 06:43:48: 20000000 INFO @ Wed, 22 Apr 2020 06:43:51: 23000000 INFO @ Wed, 22 Apr 2020 06:43:52: 14000000 INFO @ Wed, 22 Apr 2020 06:43:54: 21000000 INFO @ Wed, 22 Apr 2020 06:43:56: 24000000 INFO @ Wed, 22 Apr 2020 06:43:57: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:43:57: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:43:57: #1 total tags in treatment: 24081432 INFO @ Wed, 22 Apr 2020 06:43:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:43:57: #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 06:43:57: #1 tags after filtering in treatment: 24081330 INFO @ Wed, 22 Apr 2020 06:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:43:57: #1 finished! INFO @ Wed, 22 Apr 2020 06:43:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:43:57: 15000000 INFO @ Wed, 22 Apr 2020 06:43:59: 22000000 INFO @ Wed, 22 Apr 2020 06:43:59: #2 number of paired peaks: 5544 INFO @ Wed, 22 Apr 2020 06:43:59: start model_add_line... INFO @ Wed, 22 Apr 2020 06:43:59: start X-correlation... INFO @ Wed, 22 Apr 2020 06:43:59: end of X-cor INFO @ Wed, 22 Apr 2020 06:43:59: #2 finished! INFO @ Wed, 22 Apr 2020 06:43:59: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:43:59: #2 alternative fragment length(s) may be 37,217,396,575 bps INFO @ Wed, 22 Apr 2020 06:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.10_model.r WARNING @ Wed, 22 Apr 2020 06:43:59: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:43:59: #2 You may need to consider one of the other alternative d(s): 37,217,396,575 WARNING @ Wed, 22 Apr 2020 06:43:59: #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 06:43:59: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:44:03: 16000000 INFO @ Wed, 22 Apr 2020 06:44:04: 23000000 INFO @ Wed, 22 Apr 2020 06:44:08: 17000000 INFO @ Wed, 22 Apr 2020 06:44:09: 24000000 INFO @ Wed, 22 Apr 2020 06:44:10: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:44:10: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:44:10: #1 total tags in treatment: 24081432 INFO @ Wed, 22 Apr 2020 06:44:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:44:10: #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 06:44:10: #1 tags after filtering in treatment: 24081330 INFO @ Wed, 22 Apr 2020 06:44:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:44:10: #1 finished! INFO @ Wed, 22 Apr 2020 06:44:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:44:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:44:13: #2 number of paired peaks: 5544 INFO @ Wed, 22 Apr 2020 06:44:13: start model_add_line... INFO @ Wed, 22 Apr 2020 06:44:13: start X-correlation... INFO @ Wed, 22 Apr 2020 06:44:13: end of X-cor INFO @ Wed, 22 Apr 2020 06:44:13: #2 finished! INFO @ Wed, 22 Apr 2020 06:44:13: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:44:13: #2 alternative fragment length(s) may be 37,217,396,575 bps INFO @ Wed, 22 Apr 2020 06:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.05_model.r WARNING @ Wed, 22 Apr 2020 06:44:13: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:44:13: #2 You may need to consider one of the other alternative d(s): 37,217,396,575 WARNING @ Wed, 22 Apr 2020 06:44:13: #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 06:44:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:44:14: 18000000 INFO @ Wed, 22 Apr 2020 06:44:19: 19000000 INFO @ Wed, 22 Apr 2020 06:44:25: 20000000 INFO @ Wed, 22 Apr 2020 06:44:30: 21000000 INFO @ Wed, 22 Apr 2020 06:44:36: 22000000 INFO @ Wed, 22 Apr 2020 06:44:41: 23000000 INFO @ Wed, 22 Apr 2020 06:44:46: 24000000 INFO @ Wed, 22 Apr 2020 06:44:47: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:44:47: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:44:47: #1 total tags in treatment: 24081432 INFO @ Wed, 22 Apr 2020 06:44:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:44:47: #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 06:44:47: #1 tags after filtering in treatment: 24081330 INFO @ Wed, 22 Apr 2020 06:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:44:47: #1 finished! INFO @ Wed, 22 Apr 2020 06:44:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:44:49: #2 number of paired peaks: 5544 INFO @ Wed, 22 Apr 2020 06:44:49: start model_add_line... INFO @ Wed, 22 Apr 2020 06:44:50: start X-correlation... INFO @ Wed, 22 Apr 2020 06:44:50: end of X-cor INFO @ Wed, 22 Apr 2020 06:44:50: #2 finished! INFO @ Wed, 22 Apr 2020 06:44:50: #2 predicted fragment length is 37 bps INFO @ Wed, 22 Apr 2020 06:44:50: #2 alternative fragment length(s) may be 37,217,396,575 bps INFO @ Wed, 22 Apr 2020 06:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.20_model.r WARNING @ Wed, 22 Apr 2020 06:44:50: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:44:50: #2 You may need to consider one of the other alternative d(s): 37,217,396,575 WARNING @ Wed, 22 Apr 2020 06:44:50: #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 06:44:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:44:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:45:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:45:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:45:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.10_summits.bed INFO @ Wed, 22 Apr 2020 06:45:18: Done! pass1 - making usageList (46 chroms): 0 millis pass2 - checking and writing primary data (1257 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.05_summits.bed INFO @ Wed, 22 Apr 2020 06:45:31: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (2287 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:45:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761738/SRX5761738.20_summits.bed INFO @ Wed, 22 Apr 2020 06:46:09: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (580 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。