Job ID = 14519555 SRX = SRX9963485 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 46033347 spots for SRR13565201/SRR13565201.sra Written 46033347 spots for SRR13565201/SRR13565201.sra 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: 00:43:37 46033347 reads; of these: 46033347 (100.00%) were unpaired; of these: 4562035 (9.91%) aligned 0 times 37488242 (81.44%) aligned exactly 1 time 3983070 (8.65%) aligned >1 times 90.09% overall alignment rate Time searching: 00:43:39 Overall time: 00:43:39 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] 15875435 / 41471312 = 0.3828 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.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 @ Sat, 15 Jan 2022 17:04:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:04:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:04:45: 1000000 INFO @ Sat, 15 Jan 2022 17:04:51: 2000000 INFO @ Sat, 15 Jan 2022 17:04:56: 3000000 INFO @ Sat, 15 Jan 2022 17:05:02: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:05:08: 5000000 INFO @ Sat, 15 Jan 2022 17:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.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 @ Sat, 15 Jan 2022 17:05:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:05:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:05:14: 6000000 INFO @ Sat, 15 Jan 2022 17:05:18: 1000000 INFO @ Sat, 15 Jan 2022 17:05:21: 7000000 INFO @ Sat, 15 Jan 2022 17:05:26: 2000000 INFO @ Sat, 15 Jan 2022 17:05:28: 8000000 INFO @ Sat, 15 Jan 2022 17:05:34: 3000000 INFO @ Sat, 15 Jan 2022 17:05:35: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.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 @ Sat, 15 Jan 2022 17:05:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:05:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:05:42: 10000000 INFO @ Sat, 15 Jan 2022 17:05:43: 4000000 INFO @ Sat, 15 Jan 2022 17:05:47: 1000000 INFO @ Sat, 15 Jan 2022 17:05:50: 11000000 INFO @ Sat, 15 Jan 2022 17:05:51: 5000000 INFO @ Sat, 15 Jan 2022 17:05:54: 2000000 INFO @ Sat, 15 Jan 2022 17:05:57: 12000000 INFO @ Sat, 15 Jan 2022 17:05:59: 6000000 INFO @ Sat, 15 Jan 2022 17:06:02: 3000000 INFO @ Sat, 15 Jan 2022 17:06:04: 13000000 INFO @ Sat, 15 Jan 2022 17:06:08: 7000000 INFO @ Sat, 15 Jan 2022 17:06:09: 4000000 INFO @ Sat, 15 Jan 2022 17:06:11: 14000000 INFO @ Sat, 15 Jan 2022 17:06:16: 5000000 INFO @ Sat, 15 Jan 2022 17:06:16: 8000000 INFO @ Sat, 15 Jan 2022 17:06:18: 15000000 INFO @ Sat, 15 Jan 2022 17:06:23: 6000000 INFO @ Sat, 15 Jan 2022 17:06:24: 9000000 INFO @ Sat, 15 Jan 2022 17:06:25: 16000000 INFO @ Sat, 15 Jan 2022 17:06:30: 7000000 INFO @ Sat, 15 Jan 2022 17:06:32: 17000000 INFO @ Sat, 15 Jan 2022 17:06:33: 10000000 INFO @ Sat, 15 Jan 2022 17:06:37: 8000000 INFO @ Sat, 15 Jan 2022 17:06:39: 18000000 INFO @ Sat, 15 Jan 2022 17:06:41: 11000000 INFO @ Sat, 15 Jan 2022 17:06:44: 9000000 INFO @ Sat, 15 Jan 2022 17:06:46: 19000000 INFO @ Sat, 15 Jan 2022 17:06:50: 12000000 INFO @ Sat, 15 Jan 2022 17:06:51: 10000000 INFO @ Sat, 15 Jan 2022 17:06:54: 20000000 INFO @ Sat, 15 Jan 2022 17:06:58: 13000000 INFO @ Sat, 15 Jan 2022 17:06:58: 11000000 INFO @ Sat, 15 Jan 2022 17:07:01: 21000000 INFO @ Sat, 15 Jan 2022 17:07:06: 12000000 INFO @ Sat, 15 Jan 2022 17:07:06: 14000000 INFO @ Sat, 15 Jan 2022 17:07:08: 22000000 INFO @ Sat, 15 Jan 2022 17:07:13: 13000000 INFO @ Sat, 15 Jan 2022 17:07:15: 15000000 INFO @ Sat, 15 Jan 2022 17:07:15: 23000000 INFO @ Sat, 15 Jan 2022 17:07:20: 14000000 INFO @ Sat, 15 Jan 2022 17:07:22: 24000000 INFO @ Sat, 15 Jan 2022 17:07:23: 16000000 INFO @ Sat, 15 Jan 2022 17:07:27: 15000000 INFO @ Sat, 15 Jan 2022 17:07:29: 25000000 INFO @ Sat, 15 Jan 2022 17:07:31: 17000000 INFO @ Sat, 15 Jan 2022 17:07:34: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:07:34: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:07:34: #1 total tags in treatment: 25595877 INFO @ Sat, 15 Jan 2022 17:07:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:07:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:07:34: 16000000 INFO @ Sat, 15 Jan 2022 17:07:34: #1 tags after filtering in treatment: 25595643 INFO @ Sat, 15 Jan 2022 17:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:07:34: #1 finished! INFO @ Sat, 15 Jan 2022 17:07:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:07:38: #2 number of paired peaks: 44567 INFO @ Sat, 15 Jan 2022 17:07:38: start model_add_line... INFO @ Sat, 15 Jan 2022 17:07:38: start X-correlation... INFO @ Sat, 15 Jan 2022 17:07:38: end of X-cor INFO @ Sat, 15 Jan 2022 17:07:38: #2 finished! INFO @ Sat, 15 Jan 2022 17:07:38: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Jan 2022 17:07:38: #2 alternative fragment length(s) may be 3,202 bps INFO @ Sat, 15 Jan 2022 17:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.05_model.r INFO @ Sat, 15 Jan 2022 17:07:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:07:40: 18000000 INFO @ Sat, 15 Jan 2022 17:07:41: 17000000 INFO @ Sat, 15 Jan 2022 17:07:48: 19000000 INFO @ Sat, 15 Jan 2022 17:07:48: 18000000 INFO @ Sat, 15 Jan 2022 17:07:56: 19000000 INFO @ Sat, 15 Jan 2022 17:07:56: 20000000 INFO @ Sat, 15 Jan 2022 17:08:03: 20000000 INFO @ Sat, 15 Jan 2022 17:08:05: 21000000 INFO @ Sat, 15 Jan 2022 17:08:10: 21000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:08:13: 22000000 INFO @ Sat, 15 Jan 2022 17:08:17: 22000000 INFO @ Sat, 15 Jan 2022 17:08:21: 23000000 INFO @ Sat, 15 Jan 2022 17:08:24: 23000000 INFO @ Sat, 15 Jan 2022 17:08:29: 24000000 INFO @ Sat, 15 Jan 2022 17:08:31: 24000000 INFO @ Sat, 15 Jan 2022 17:08:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:08:37: 25000000 INFO @ Sat, 15 Jan 2022 17:08:39: 25000000 INFO @ Sat, 15 Jan 2022 17:08:42: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:08:42: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:08:42: #1 total tags in treatment: 25595877 INFO @ Sat, 15 Jan 2022 17:08:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:08:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:08:42: #1 tags after filtering in treatment: 25595643 INFO @ Sat, 15 Jan 2022 17:08:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:08:42: #1 finished! INFO @ Sat, 15 Jan 2022 17:08:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:08:43: #1 tag size is determined as 76 bps INFO @ Sat, 15 Jan 2022 17:08:43: #1 tag size = 76 INFO @ Sat, 15 Jan 2022 17:08:43: #1 total tags in treatment: 25595877 INFO @ Sat, 15 Jan 2022 17:08:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:08:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:08:43: #1 tags after filtering in treatment: 25595643 INFO @ Sat, 15 Jan 2022 17:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:08:43: #1 finished! INFO @ Sat, 15 Jan 2022 17:08:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:08:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:08:46: #2 number of paired peaks: 44567 INFO @ Sat, 15 Jan 2022 17:08:46: start model_add_line... INFO @ Sat, 15 Jan 2022 17:08:46: start X-correlation... INFO @ Sat, 15 Jan 2022 17:08:46: end of X-cor INFO @ Sat, 15 Jan 2022 17:08:46: #2 finished! INFO @ Sat, 15 Jan 2022 17:08:46: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Jan 2022 17:08:46: #2 alternative fragment length(s) may be 3,202 bps INFO @ Sat, 15 Jan 2022 17:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.10_model.r INFO @ Sat, 15 Jan 2022 17:08:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:08:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:08:47: #2 number of paired peaks: 44567 INFO @ Sat, 15 Jan 2022 17:08:47: start model_add_line... INFO @ Sat, 15 Jan 2022 17:08:47: start X-correlation... INFO @ Sat, 15 Jan 2022 17:08:47: end of X-cor INFO @ Sat, 15 Jan 2022 17:08:47: #2 finished! INFO @ Sat, 15 Jan 2022 17:08:47: #2 predicted fragment length is 202 bps INFO @ Sat, 15 Jan 2022 17:08:47: #2 alternative fragment length(s) may be 3,202 bps INFO @ Sat, 15 Jan 2022 17:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.20_model.r INFO @ Sat, 15 Jan 2022 17:08:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:08:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.05_summits.bed INFO @ Sat, 15 Jan 2022 17:09:07: Done! pass1 - making usageList (131 chroms): 3 millis pass2 - checking and writing primary data (22915 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:09:43: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:09:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:10:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.20_summits.bed INFO @ Sat, 15 Jan 2022 17:10:13: Done! pass1 - making usageList (105 chroms): 3 millis pass2 - checking and writing primary data (17687 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9963485/SRX9963485.10_summits.bed INFO @ Sat, 15 Jan 2022 17:10:19: Done! pass1 - making usageList (117 chroms): 4 millis pass2 - checking and writing primary data (20241 records, 4 fields): 22 millis CompletedMACS2peakCalling