Job ID = 7096649 SRX = SRX3919489 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 53658128 spots for SRR6978717/SRR6978717.sra Written 53658128 spots for SRR6978717/SRR6978717.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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:31 53658128 reads; of these: 53658128 (100.00%) were unpaired; of these: 14649529 (27.30%) aligned 0 times 28751740 (53.58%) aligned exactly 1 time 10256859 (19.12%) aligned >1 times 72.70% overall alignment rate Time searching: 00:29:36 Overall time: 00:29:36 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] 1665173 / 39008599 = 0.0427 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 Jul 2020 11:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.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 Jul 2020 11:40:08: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:40:08: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:40:14: 1000000 INFO @ Wed, 22 Jul 2020 11:40:20: 2000000 INFO @ Wed, 22 Jul 2020 11:40:26: 3000000 INFO @ Wed, 22 Jul 2020 11:40:32: 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 Jul 2020 11:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.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 Jul 2020 11:40:37: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:40:37: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:40:38: 5000000 INFO @ Wed, 22 Jul 2020 11:40:45: 6000000 INFO @ Wed, 22 Jul 2020 11:40:45: 1000000 INFO @ Wed, 22 Jul 2020 11:40:52: 7000000 INFO @ Wed, 22 Jul 2020 11:40:53: 2000000 INFO @ Wed, 22 Jul 2020 11:40:59: 8000000 INFO @ Wed, 22 Jul 2020 11:41:01: 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 Jul 2020 11:41:07: 9000000 INFO @ Wed, 22 Jul 2020 11:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.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 Jul 2020 11:41:07: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:41:07: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:41:09: 4000000 INFO @ Wed, 22 Jul 2020 11:41:14: 10000000 INFO @ Wed, 22 Jul 2020 11:41:16: 1000000 INFO @ Wed, 22 Jul 2020 11:41:17: 5000000 INFO @ Wed, 22 Jul 2020 11:41:22: 11000000 INFO @ Wed, 22 Jul 2020 11:41:23: 2000000 INFO @ Wed, 22 Jul 2020 11:41:26: 6000000 INFO @ Wed, 22 Jul 2020 11:41:30: 12000000 INFO @ Wed, 22 Jul 2020 11:41:31: 3000000 INFO @ Wed, 22 Jul 2020 11:41:34: 7000000 INFO @ Wed, 22 Jul 2020 11:41:38: 13000000 INFO @ Wed, 22 Jul 2020 11:41:40: 4000000 INFO @ Wed, 22 Jul 2020 11:41:42: 8000000 INFO @ Wed, 22 Jul 2020 11:41:46: 14000000 INFO @ Wed, 22 Jul 2020 11:41:47: 5000000 INFO @ Wed, 22 Jul 2020 11:41:50: 9000000 INFO @ Wed, 22 Jul 2020 11:41:54: 15000000 INFO @ Wed, 22 Jul 2020 11:41:55: 6000000 INFO @ Wed, 22 Jul 2020 11:41:58: 10000000 INFO @ Wed, 22 Jul 2020 11:42:02: 16000000 INFO @ Wed, 22 Jul 2020 11:42:03: 7000000 INFO @ Wed, 22 Jul 2020 11:42:07: 11000000 INFO @ Wed, 22 Jul 2020 11:42:10: 17000000 INFO @ Wed, 22 Jul 2020 11:42:12: 8000000 INFO @ Wed, 22 Jul 2020 11:42:15: 12000000 INFO @ Wed, 22 Jul 2020 11:42:18: 18000000 INFO @ Wed, 22 Jul 2020 11:42:20: 9000000 INFO @ Wed, 22 Jul 2020 11:42:23: 13000000 INFO @ Wed, 22 Jul 2020 11:42:26: 19000000 INFO @ Wed, 22 Jul 2020 11:42:28: 10000000 INFO @ Wed, 22 Jul 2020 11:42:31: 14000000 INFO @ Wed, 22 Jul 2020 11:42:33: 20000000 INFO @ Wed, 22 Jul 2020 11:42:36: 11000000 INFO @ Wed, 22 Jul 2020 11:42:39: 15000000 INFO @ Wed, 22 Jul 2020 11:42:42: 21000000 INFO @ Wed, 22 Jul 2020 11:42:44: 12000000 INFO @ Wed, 22 Jul 2020 11:42:47: 16000000 INFO @ Wed, 22 Jul 2020 11:42:50: 22000000 INFO @ Wed, 22 Jul 2020 11:42:52: 13000000 INFO @ Wed, 22 Jul 2020 11:42:56: 17000000 INFO @ Wed, 22 Jul 2020 11:42:58: 23000000 INFO @ Wed, 22 Jul 2020 11:43:01: 14000000 INFO @ Wed, 22 Jul 2020 11:43:04: 18000000 INFO @ Wed, 22 Jul 2020 11:43:06: 24000000 INFO @ Wed, 22 Jul 2020 11:43:08: 15000000 INFO @ Wed, 22 Jul 2020 11:43:11: 19000000 INFO @ Wed, 22 Jul 2020 11:43:14: 25000000 INFO @ Wed, 22 Jul 2020 11:43:16: 16000000 INFO @ Wed, 22 Jul 2020 11:43:19: 20000000 INFO @ Wed, 22 Jul 2020 11:43:22: 26000000 INFO @ Wed, 22 Jul 2020 11:43:23: 17000000 INFO @ Wed, 22 Jul 2020 11:43:27: 21000000 INFO @ Wed, 22 Jul 2020 11:43:30: 27000000 INFO @ Wed, 22 Jul 2020 11:43:31: 18000000 INFO @ Wed, 22 Jul 2020 11:43:36: 22000000 INFO @ Wed, 22 Jul 2020 11:43:38: 28000000 INFO @ Wed, 22 Jul 2020 11:43:39: 19000000 INFO @ Wed, 22 Jul 2020 11:43:44: 23000000 INFO @ Wed, 22 Jul 2020 11:43:45: 29000000 INFO @ Wed, 22 Jul 2020 11:43:47: 20000000 INFO @ Wed, 22 Jul 2020 11:43:51: 24000000 INFO @ Wed, 22 Jul 2020 11:43:52: 30000000 INFO @ Wed, 22 Jul 2020 11:43:55: 21000000 INFO @ Wed, 22 Jul 2020 11:43:59: 25000000 INFO @ Wed, 22 Jul 2020 11:44:00: 31000000 INFO @ Wed, 22 Jul 2020 11:44:03: 22000000 INFO @ Wed, 22 Jul 2020 11:44:07: 26000000 INFO @ Wed, 22 Jul 2020 11:44:07: 32000000 INFO @ Wed, 22 Jul 2020 11:44:10: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 11:44:14: 27000000 INFO @ Wed, 22 Jul 2020 11:44:15: 33000000 INFO @ Wed, 22 Jul 2020 11:44:18: 24000000 INFO @ Wed, 22 Jul 2020 11:44:21: 28000000 INFO @ Wed, 22 Jul 2020 11:44:22: 34000000 INFO @ Wed, 22 Jul 2020 11:44:25: 25000000 INFO @ Wed, 22 Jul 2020 11:44:28: 29000000 INFO @ Wed, 22 Jul 2020 11:44:29: 35000000 INFO @ Wed, 22 Jul 2020 11:44:33: 26000000 INFO @ Wed, 22 Jul 2020 11:44:35: 30000000 INFO @ Wed, 22 Jul 2020 11:44:36: 36000000 INFO @ Wed, 22 Jul 2020 11:44:40: 27000000 INFO @ Wed, 22 Jul 2020 11:44:42: 31000000 INFO @ Wed, 22 Jul 2020 11:44:43: 37000000 INFO @ Wed, 22 Jul 2020 11:44:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:44:45: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:44:45: #1 total tags in treatment: 37343426 INFO @ Wed, 22 Jul 2020 11:44:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:44:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:44:46: #1 tags after filtering in treatment: 37343334 INFO @ Wed, 22 Jul 2020 11:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:44:46: #1 finished! INFO @ Wed, 22 Jul 2020 11:44:46: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:44:47: 28000000 INFO @ Wed, 22 Jul 2020 11:44:49: 32000000 INFO @ Wed, 22 Jul 2020 11:44:49: #2 number of paired peaks: 4078 INFO @ Wed, 22 Jul 2020 11:44:49: start model_add_line... INFO @ Wed, 22 Jul 2020 11:44:50: start X-correlation... INFO @ Wed, 22 Jul 2020 11:44:50: end of X-cor INFO @ Wed, 22 Jul 2020 11:44:50: #2 finished! INFO @ Wed, 22 Jul 2020 11:44:50: #2 predicted fragment length is 49 bps INFO @ Wed, 22 Jul 2020 11:44:50: #2 alternative fragment length(s) may be 49,221,398 bps INFO @ Wed, 22 Jul 2020 11:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.05_model.r WARNING @ Wed, 22 Jul 2020 11:44:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:44:50: #2 You may need to consider one of the other alternative d(s): 49,221,398 WARNING @ Wed, 22 Jul 2020 11:44:50: #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 Jul 2020 11:44:50: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:44:54: 29000000 INFO @ Wed, 22 Jul 2020 11:44:56: 33000000 INFO @ Wed, 22 Jul 2020 11:45:01: 30000000 INFO @ Wed, 22 Jul 2020 11:45:03: 34000000 INFO @ Wed, 22 Jul 2020 11:45:08: 31000000 INFO @ Wed, 22 Jul 2020 11:45:11: 35000000 INFO @ Wed, 22 Jul 2020 11:45:15: 32000000 INFO @ Wed, 22 Jul 2020 11:45:18: 36000000 INFO @ Wed, 22 Jul 2020 11:45:22: 33000000 INFO @ Wed, 22 Jul 2020 11:45:25: 37000000 INFO @ Wed, 22 Jul 2020 11:45:28: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:45:28: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:45:28: #1 total tags in treatment: 37343426 INFO @ Wed, 22 Jul 2020 11:45:28: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:45:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:45:29: #1 tags after filtering in treatment: 37343334 INFO @ Wed, 22 Jul 2020 11:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:45:29: #1 finished! INFO @ Wed, 22 Jul 2020 11:45:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:45:29: 34000000 INFO @ Wed, 22 Jul 2020 11:45:32: #2 number of paired peaks: 4078 INFO @ Wed, 22 Jul 2020 11:45:32: start model_add_line... INFO @ Wed, 22 Jul 2020 11:45:33: start X-correlation... INFO @ Wed, 22 Jul 2020 11:45:33: end of X-cor INFO @ Wed, 22 Jul 2020 11:45:33: #2 finished! INFO @ Wed, 22 Jul 2020 11:45:33: #2 predicted fragment length is 49 bps INFO @ Wed, 22 Jul 2020 11:45:33: #2 alternative fragment length(s) may be 49,221,398 bps INFO @ Wed, 22 Jul 2020 11:45:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.10_model.r WARNING @ Wed, 22 Jul 2020 11:45:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:45:33: #2 You may need to consider one of the other alternative d(s): 49,221,398 WARNING @ Wed, 22 Jul 2020 11:45:33: #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 Jul 2020 11:45:33: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:45:36: 35000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 11:45:42: 36000000 INFO @ Wed, 22 Jul 2020 11:45:48: 37000000 INFO @ Wed, 22 Jul 2020 11:45:50: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 11:45:50: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 11:45:50: #1 total tags in treatment: 37343426 INFO @ Wed, 22 Jul 2020 11:45:50: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:45:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:45:51: #1 tags after filtering in treatment: 37343334 INFO @ Wed, 22 Jul 2020 11:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:45:51: #1 finished! INFO @ Wed, 22 Jul 2020 11:45:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:45:54: #2 number of paired peaks: 4078 INFO @ Wed, 22 Jul 2020 11:45:54: start model_add_line... INFO @ Wed, 22 Jul 2020 11:45:54: start X-correlation... INFO @ Wed, 22 Jul 2020 11:45:54: end of X-cor INFO @ Wed, 22 Jul 2020 11:45:54: #2 finished! INFO @ Wed, 22 Jul 2020 11:45:54: #2 predicted fragment length is 49 bps INFO @ Wed, 22 Jul 2020 11:45:54: #2 alternative fragment length(s) may be 49,221,398 bps INFO @ Wed, 22 Jul 2020 11:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.20_model.r WARNING @ Wed, 22 Jul 2020 11:45:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:45:54: #2 You may need to consider one of the other alternative d(s): 49,221,398 WARNING @ Wed, 22 Jul 2020 11:45:54: #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 Jul 2020 11:45:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:45:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:46:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:46:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.05_peaks.xls INFO @ Wed, 22 Jul 2020 11:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.05_summits.bed INFO @ Wed, 22 Jul 2020 11:46:56: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (2050 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:47:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.10_peaks.xls INFO @ Wed, 22 Jul 2020 11:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.10_summits.bed INFO @ Wed, 22 Jul 2020 11:47:39: Done! pass1 - making usageList (63 chroms): 0 millis pass2 - checking and writing primary data (1208 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.20_peaks.xls INFO @ Wed, 22 Jul 2020 11:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3919489/SRX3919489.20_summits.bed INFO @ Wed, 22 Jul 2020 11:48:00: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (607 records, 4 fields): 4 millis CompletedMACS2peakCalling