Job ID = 8184458 SRX = SRX8047595 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:23:39 prefetch.2.10.7: 1) Downloading 'SRR11471319'... 2020-08-10T03:23:39 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:25:52 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:25:52 prefetch.2.10.7: 1) 'SRR11471319' was downloaded successfully Read 55357254 spots for SRR11471319/SRR11471319.sra Written 55357254 spots for SRR11471319/SRR11471319.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:08:57 55357254 reads; of these: 55357254 (100.00%) were unpaired; of these: 2239701 (4.05%) aligned 0 times 37883597 (68.43%) aligned exactly 1 time 15233956 (27.52%) aligned >1 times 95.95% overall alignment rate Time searching: 01:09:00 Overall time: 01:09:00 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 24 files... [bam_rmdupse_core] 15609462 / 53117553 = 0.2939 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 13:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.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 13:49:53: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:49:53: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:49:59: 1000000 INFO @ Mon, 10 Aug 2020 13:50:04: 2000000 INFO @ Mon, 10 Aug 2020 13:50:09: 3000000 INFO @ Mon, 10 Aug 2020 13:50:15: 4000000 INFO @ Mon, 10 Aug 2020 13:50:20: 5000000 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 13:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.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 13:50:23: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:50:23: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:50:25: 6000000 INFO @ Mon, 10 Aug 2020 13:50:28: 1000000 INFO @ Mon, 10 Aug 2020 13:50:31: 7000000 INFO @ Mon, 10 Aug 2020 13:50:33: 2000000 INFO @ Mon, 10 Aug 2020 13:50:36: 8000000 INFO @ Mon, 10 Aug 2020 13:50:38: 3000000 INFO @ Mon, 10 Aug 2020 13:50:42: 9000000 INFO @ Mon, 10 Aug 2020 13:50:43: 4000000 INFO @ Mon, 10 Aug 2020 13:50:47: 10000000 INFO @ Mon, 10 Aug 2020 13:50:48: 5000000 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 13:50:52: 6000000 INFO @ Mon, 10 Aug 2020 13:50:52: 11000000 INFO @ Mon, 10 Aug 2020 13:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.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 13:50:53: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:50:53: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:50:57: 7000000 INFO @ Mon, 10 Aug 2020 13:50:58: 12000000 INFO @ Mon, 10 Aug 2020 13:50:59: 1000000 INFO @ Mon, 10 Aug 2020 13:51:02: 8000000 INFO @ Mon, 10 Aug 2020 13:51:03: 13000000 INFO @ Mon, 10 Aug 2020 13:51:04: 2000000 INFO @ Mon, 10 Aug 2020 13:51:07: 9000000 INFO @ Mon, 10 Aug 2020 13:51:09: 14000000 INFO @ Mon, 10 Aug 2020 13:51:10: 3000000 INFO @ Mon, 10 Aug 2020 13:51:12: 10000000 INFO @ Mon, 10 Aug 2020 13:51:14: 15000000 INFO @ Mon, 10 Aug 2020 13:51:15: 4000000 INFO @ Mon, 10 Aug 2020 13:51:17: 11000000 INFO @ Mon, 10 Aug 2020 13:51:20: 16000000 INFO @ Mon, 10 Aug 2020 13:51:20: 5000000 INFO @ Mon, 10 Aug 2020 13:51:22: 12000000 INFO @ Mon, 10 Aug 2020 13:51:25: 17000000 INFO @ Mon, 10 Aug 2020 13:51:26: 6000000 INFO @ Mon, 10 Aug 2020 13:51:27: 13000000 INFO @ Mon, 10 Aug 2020 13:51:31: 18000000 INFO @ Mon, 10 Aug 2020 13:51:31: 7000000 INFO @ Mon, 10 Aug 2020 13:51:32: 14000000 INFO @ Mon, 10 Aug 2020 13:51:36: 19000000 INFO @ Mon, 10 Aug 2020 13:51:36: 15000000 INFO @ Mon, 10 Aug 2020 13:51:37: 8000000 INFO @ Mon, 10 Aug 2020 13:51:41: 16000000 INFO @ Mon, 10 Aug 2020 13:51:41: 20000000 INFO @ Mon, 10 Aug 2020 13:51:42: 9000000 INFO @ Mon, 10 Aug 2020 13:51:46: 17000000 INFO @ Mon, 10 Aug 2020 13:51:47: 21000000 INFO @ Mon, 10 Aug 2020 13:51:47: 10000000 INFO @ Mon, 10 Aug 2020 13:51:51: 18000000 INFO @ Mon, 10 Aug 2020 13:51:52: 22000000 INFO @ Mon, 10 Aug 2020 13:51:53: 11000000 INFO @ Mon, 10 Aug 2020 13:51:56: 19000000 INFO @ Mon, 10 Aug 2020 13:51:58: 23000000 INFO @ Mon, 10 Aug 2020 13:51:58: 12000000 INFO @ Mon, 10 Aug 2020 13:52:01: 20000000 INFO @ Mon, 10 Aug 2020 13:52:03: 24000000 INFO @ Mon, 10 Aug 2020 13:52:03: 13000000 INFO @ Mon, 10 Aug 2020 13:52:06: 21000000 INFO @ Mon, 10 Aug 2020 13:52:09: 25000000 INFO @ Mon, 10 Aug 2020 13:52:09: 14000000 INFO @ Mon, 10 Aug 2020 13:52:10: 22000000 INFO @ Mon, 10 Aug 2020 13:52:14: 26000000 INFO @ Mon, 10 Aug 2020 13:52:14: 15000000 INFO @ Mon, 10 Aug 2020 13:52:15: 23000000 INFO @ Mon, 10 Aug 2020 13:52:20: 27000000 INFO @ Mon, 10 Aug 2020 13:52:20: 16000000 INFO @ Mon, 10 Aug 2020 13:52:20: 24000000 INFO @ Mon, 10 Aug 2020 13:52:25: 28000000 INFO @ Mon, 10 Aug 2020 13:52:25: 17000000 INFO @ Mon, 10 Aug 2020 13:52:25: 25000000 INFO @ Mon, 10 Aug 2020 13:52:30: 26000000 INFO @ Mon, 10 Aug 2020 13:52:30: 29000000 INFO @ Mon, 10 Aug 2020 13:52:30: 18000000 INFO @ Mon, 10 Aug 2020 13:52:35: 27000000 INFO @ Mon, 10 Aug 2020 13:52:36: 19000000 INFO @ Mon, 10 Aug 2020 13:52:36: 30000000 INFO @ Mon, 10 Aug 2020 13:52:39: 28000000 INFO @ Mon, 10 Aug 2020 13:52:41: 20000000 INFO @ Mon, 10 Aug 2020 13:52:41: 31000000 INFO @ Mon, 10 Aug 2020 13:52:44: 29000000 INFO @ Mon, 10 Aug 2020 13:52:47: 32000000 INFO @ Mon, 10 Aug 2020 13:52:47: 21000000 INFO @ Mon, 10 Aug 2020 13:52:49: 30000000 INFO @ Mon, 10 Aug 2020 13:52:52: 33000000 INFO @ Mon, 10 Aug 2020 13:52:52: 22000000 INFO @ Mon, 10 Aug 2020 13:52:54: 31000000 INFO @ Mon, 10 Aug 2020 13:52:57: 34000000 INFO @ Mon, 10 Aug 2020 13:52:58: 23000000 INFO @ Mon, 10 Aug 2020 13:52:59: 32000000 INFO @ Mon, 10 Aug 2020 13:53:03: 35000000 INFO @ Mon, 10 Aug 2020 13:53:03: 24000000 INFO @ Mon, 10 Aug 2020 13:53:04: 33000000 INFO @ Mon, 10 Aug 2020 13:53:08: 34000000 INFO @ Mon, 10 Aug 2020 13:53:08: 36000000 INFO @ Mon, 10 Aug 2020 13:53:09: 25000000 INFO @ Mon, 10 Aug 2020 13:53:13: 35000000 INFO @ Mon, 10 Aug 2020 13:53:14: 37000000 INFO @ Mon, 10 Aug 2020 13:53:14: 26000000 INFO @ Mon, 10 Aug 2020 13:53:17: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:53:17: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:53:17: #1 total tags in treatment: 37508091 INFO @ Mon, 10 Aug 2020 13:53:17: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:53:17: #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 13:53:18: #1 tags after filtering in treatment: 37508017 INFO @ Mon, 10 Aug 2020 13:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:53:18: #1 finished! INFO @ Mon, 10 Aug 2020 13:53:18: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:53:18: 36000000 INFO @ Mon, 10 Aug 2020 13:53:19: 27000000 INFO @ Mon, 10 Aug 2020 13:53:21: #2 number of paired peaks: 11936 INFO @ Mon, 10 Aug 2020 13:53:21: start model_add_line... INFO @ Mon, 10 Aug 2020 13:53:21: start X-correlation... INFO @ Mon, 10 Aug 2020 13:53:21: end of X-cor INFO @ Mon, 10 Aug 2020 13:53:21: #2 finished! INFO @ Mon, 10 Aug 2020 13:53:21: #2 predicted fragment length is 61 bps INFO @ Mon, 10 Aug 2020 13:53:21: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 10 Aug 2020 13:53:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.05_model.r WARNING @ Mon, 10 Aug 2020 13:53:21: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:53:21: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 10 Aug 2020 13:53:21: #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 13:53:21: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:53:23: 37000000 INFO @ Mon, 10 Aug 2020 13:53:25: 28000000 INFO @ Mon, 10 Aug 2020 13:53:26: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:53:26: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:53:26: #1 total tags in treatment: 37508091 INFO @ Mon, 10 Aug 2020 13:53:26: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:53:26: #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 13:53:26: #1 tags after filtering in treatment: 37508017 INFO @ Mon, 10 Aug 2020 13:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:53:26: #1 finished! INFO @ Mon, 10 Aug 2020 13:53:26: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:53:30: #2 number of paired peaks: 11936 INFO @ Mon, 10 Aug 2020 13:53:30: start model_add_line... INFO @ Mon, 10 Aug 2020 13:53:30: start X-correlation... INFO @ Mon, 10 Aug 2020 13:53:30: end of X-cor INFO @ Mon, 10 Aug 2020 13:53:30: #2 finished! INFO @ Mon, 10 Aug 2020 13:53:30: #2 predicted fragment length is 61 bps INFO @ Mon, 10 Aug 2020 13:53:30: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 10 Aug 2020 13:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.10_model.r WARNING @ Mon, 10 Aug 2020 13:53:30: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:53:30: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 10 Aug 2020 13:53:30: #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 13:53:30: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:53:30: 29000000 INFO @ Mon, 10 Aug 2020 13:53:35: 30000000 INFO @ Mon, 10 Aug 2020 13:53:41: 31000000 INFO @ Mon, 10 Aug 2020 13:53:46: 32000000 INFO @ Mon, 10 Aug 2020 13:53:51: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:53:57: 34000000 INFO @ Mon, 10 Aug 2020 13:54:02: 35000000 INFO @ Mon, 10 Aug 2020 13:54:07: 36000000 INFO @ Mon, 10 Aug 2020 13:54:12: 37000000 INFO @ Mon, 10 Aug 2020 13:54:16: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:54:16: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:54:16: #1 total tags in treatment: 37508091 INFO @ Mon, 10 Aug 2020 13:54:16: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:54:16: #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 13:54:16: #1 tags after filtering in treatment: 37508017 INFO @ Mon, 10 Aug 2020 13:54:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:54:16: #1 finished! INFO @ Mon, 10 Aug 2020 13:54:16: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:54:20: #2 number of paired peaks: 11936 INFO @ Mon, 10 Aug 2020 13:54:20: start model_add_line... INFO @ Mon, 10 Aug 2020 13:54:20: start X-correlation... INFO @ Mon, 10 Aug 2020 13:54:20: end of X-cor INFO @ Mon, 10 Aug 2020 13:54:20: #2 finished! INFO @ Mon, 10 Aug 2020 13:54:20: #2 predicted fragment length is 61 bps INFO @ Mon, 10 Aug 2020 13:54:20: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 10 Aug 2020 13:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.20_model.r WARNING @ Mon, 10 Aug 2020 13:54:20: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:54:20: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 10 Aug 2020 13:54:20: #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 13:54:20: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:54:42: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:54:55: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.05_summits.bed INFO @ Mon, 10 Aug 2020 13:55:26: Done! pass1 - making usageList (121 chroms): 4 millis pass2 - checking and writing primary data (17866 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.10_summits.bed INFO @ Mon, 10 Aug 2020 13:55:37: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (6075 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:55:44: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047595/SRX8047595.20_summits.bed INFO @ Mon, 10 Aug 2020 13:56:28: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1697 records, 4 fields): 6 millis CompletedMACS2peakCalling