Job ID = 10223568 SRX = ERX2745104 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T17:57:19 prefetch.2.10.7: 1) Downloading 'ERR2731879'... 2020-10-15T17:57:19 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T17:59:16 prefetch.2.10.7: HTTPS download succeed 2020-10-15T17:59:16 prefetch.2.10.7: 1) 'ERR2731879' was downloaded successfully Read 78576976 spots for ERR2731879/ERR2731879.sra Written 78576976 spots for ERR2731879/ERR2731879.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:50:26 78576976 reads; of these: 78576976 (100.00%) were unpaired; of these: 2375214 (3.02%) aligned 0 times 66670735 (84.85%) aligned exactly 1 time 9531027 (12.13%) aligned >1 times 96.98% overall alignment rate Time searching: 00:50:30 Overall time: 00:50:30 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 32 files... [bam_rmdupse_core] 25373561 / 76201762 = 0.3330 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 @ Fri, 16 Oct 2020 04:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.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 @ Fri, 16 Oct 2020 04:05:14: #1 read tag files... INFO @ Fri, 16 Oct 2020 04:05:14: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 04:05:19: 1000000 INFO @ Fri, 16 Oct 2020 04:05:24: 2000000 INFO @ Fri, 16 Oct 2020 04:05:28: 3000000 INFO @ Fri, 16 Oct 2020 04:05:33: 4000000 INFO @ Fri, 16 Oct 2020 04:05:37: 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 @ Fri, 16 Oct 2020 04:05:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.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 @ Fri, 16 Oct 2020 04:05:40: #1 read tag files... INFO @ Fri, 16 Oct 2020 04:05:40: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 04:05:42: 6000000 INFO @ Fri, 16 Oct 2020 04:05:45: 1000000 INFO @ Fri, 16 Oct 2020 04:05:47: 7000000 INFO @ Fri, 16 Oct 2020 04:05:50: 2000000 INFO @ Fri, 16 Oct 2020 04:05:51: 8000000 INFO @ Fri, 16 Oct 2020 04:05:54: 3000000 INFO @ Fri, 16 Oct 2020 04:05:56: 9000000 INFO @ Fri, 16 Oct 2020 04:05:59: 4000000 INFO @ Fri, 16 Oct 2020 04:06:00: 10000000 INFO @ Fri, 16 Oct 2020 04:06:04: 5000000 INFO @ Fri, 16 Oct 2020 04:06:05: 11000000 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 @ Fri, 16 Oct 2020 04:06:09: 6000000 INFO @ Fri, 16 Oct 2020 04:06:10: 12000000 INFO @ Fri, 16 Oct 2020 04:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.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 @ Fri, 16 Oct 2020 04:06:10: #1 read tag files... INFO @ Fri, 16 Oct 2020 04:06:10: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 04:06:14: 7000000 INFO @ Fri, 16 Oct 2020 04:06:14: 13000000 INFO @ Fri, 16 Oct 2020 04:06:15: 1000000 INFO @ Fri, 16 Oct 2020 04:06:18: 8000000 INFO @ Fri, 16 Oct 2020 04:06:19: 14000000 INFO @ Fri, 16 Oct 2020 04:06:21: 2000000 INFO @ Fri, 16 Oct 2020 04:06:23: 9000000 INFO @ Fri, 16 Oct 2020 04:06:24: 15000000 INFO @ Fri, 16 Oct 2020 04:06:26: 3000000 INFO @ Fri, 16 Oct 2020 04:06:28: 10000000 INFO @ Fri, 16 Oct 2020 04:06:29: 16000000 INFO @ Fri, 16 Oct 2020 04:06:32: 4000000 INFO @ Fri, 16 Oct 2020 04:06:32: 11000000 INFO @ Fri, 16 Oct 2020 04:06:33: 17000000 INFO @ Fri, 16 Oct 2020 04:06:37: 12000000 INFO @ Fri, 16 Oct 2020 04:06:37: 5000000 INFO @ Fri, 16 Oct 2020 04:06:38: 18000000 INFO @ Fri, 16 Oct 2020 04:06:41: 13000000 INFO @ Fri, 16 Oct 2020 04:06:42: 19000000 INFO @ Fri, 16 Oct 2020 04:06:43: 6000000 INFO @ Fri, 16 Oct 2020 04:06:46: 14000000 INFO @ Fri, 16 Oct 2020 04:06:47: 20000000 INFO @ Fri, 16 Oct 2020 04:06:48: 7000000 INFO @ Fri, 16 Oct 2020 04:06:51: 15000000 INFO @ Fri, 16 Oct 2020 04:06:51: 21000000 INFO @ Fri, 16 Oct 2020 04:06:53: 8000000 INFO @ Fri, 16 Oct 2020 04:06:55: 16000000 INFO @ Fri, 16 Oct 2020 04:06:56: 22000000 INFO @ Fri, 16 Oct 2020 04:06:58: 9000000 INFO @ Fri, 16 Oct 2020 04:07:00: 17000000 INFO @ Fri, 16 Oct 2020 04:07:01: 23000000 INFO @ Fri, 16 Oct 2020 04:07:03: 10000000 INFO @ Fri, 16 Oct 2020 04:07:04: 18000000 INFO @ Fri, 16 Oct 2020 04:07:05: 24000000 INFO @ Fri, 16 Oct 2020 04:07:09: 11000000 INFO @ Fri, 16 Oct 2020 04:07:09: 19000000 INFO @ Fri, 16 Oct 2020 04:07:10: 25000000 INFO @ Fri, 16 Oct 2020 04:07:13: 20000000 INFO @ Fri, 16 Oct 2020 04:07:14: 12000000 INFO @ Fri, 16 Oct 2020 04:07:14: 26000000 INFO @ Fri, 16 Oct 2020 04:07:18: 21000000 INFO @ Fri, 16 Oct 2020 04:07:19: 27000000 INFO @ Fri, 16 Oct 2020 04:07:19: 13000000 INFO @ Fri, 16 Oct 2020 04:07:23: 22000000 INFO @ Fri, 16 Oct 2020 04:07:23: 28000000 INFO @ Fri, 16 Oct 2020 04:07:24: 14000000 INFO @ Fri, 16 Oct 2020 04:07:27: 23000000 INFO @ Fri, 16 Oct 2020 04:07:28: 29000000 INFO @ Fri, 16 Oct 2020 04:07:29: 15000000 INFO @ Fri, 16 Oct 2020 04:07:32: 24000000 INFO @ Fri, 16 Oct 2020 04:07:33: 30000000 INFO @ Fri, 16 Oct 2020 04:07:35: 16000000 INFO @ Fri, 16 Oct 2020 04:07:37: 25000000 INFO @ Fri, 16 Oct 2020 04:07:37: 31000000 INFO @ Fri, 16 Oct 2020 04:07:40: 17000000 INFO @ Fri, 16 Oct 2020 04:07:42: 32000000 INFO @ Fri, 16 Oct 2020 04:07:42: 26000000 INFO @ Fri, 16 Oct 2020 04:07:45: 18000000 INFO @ Fri, 16 Oct 2020 04:07:46: 33000000 INFO @ Fri, 16 Oct 2020 04:07:47: 27000000 INFO @ Fri, 16 Oct 2020 04:07:50: 19000000 INFO @ Fri, 16 Oct 2020 04:07:51: 34000000 INFO @ Fri, 16 Oct 2020 04:07:51: 28000000 INFO @ Fri, 16 Oct 2020 04:07:55: 20000000 INFO @ Fri, 16 Oct 2020 04:07:55: 35000000 INFO @ Fri, 16 Oct 2020 04:07:56: 29000000 INFO @ Fri, 16 Oct 2020 04:08:00: 36000000 INFO @ Fri, 16 Oct 2020 04:08:00: 21000000 INFO @ Fri, 16 Oct 2020 04:08:01: 30000000 INFO @ Fri, 16 Oct 2020 04:08:05: 37000000 INFO @ Fri, 16 Oct 2020 04:08:05: 31000000 INFO @ Fri, 16 Oct 2020 04:08:05: 22000000 INFO @ Fri, 16 Oct 2020 04:08:09: 38000000 INFO @ Fri, 16 Oct 2020 04:08:10: 32000000 INFO @ Fri, 16 Oct 2020 04:08:11: 23000000 INFO @ Fri, 16 Oct 2020 04:08:14: 39000000 INFO @ Fri, 16 Oct 2020 04:08:14: 33000000 INFO @ Fri, 16 Oct 2020 04:08:16: 24000000 INFO @ Fri, 16 Oct 2020 04:08:18: 40000000 INFO @ Fri, 16 Oct 2020 04:08:19: 34000000 INFO @ Fri, 16 Oct 2020 04:08:21: 25000000 INFO @ Fri, 16 Oct 2020 04:08:23: 41000000 INFO @ Fri, 16 Oct 2020 04:08:24: 35000000 INFO @ Fri, 16 Oct 2020 04:08:26: 26000000 INFO @ Fri, 16 Oct 2020 04:08:27: 42000000 INFO @ Fri, 16 Oct 2020 04:08:28: 36000000 INFO @ Fri, 16 Oct 2020 04:08:31: 27000000 INFO @ Fri, 16 Oct 2020 04:08:32: 43000000 INFO @ Fri, 16 Oct 2020 04:08:33: 37000000 INFO @ Fri, 16 Oct 2020 04:08:36: 28000000 INFO @ Fri, 16 Oct 2020 04:08:36: 44000000 INFO @ Fri, 16 Oct 2020 04:08:37: 38000000 INFO @ Fri, 16 Oct 2020 04:08:41: 45000000 INFO @ Fri, 16 Oct 2020 04:08:41: 29000000 INFO @ Fri, 16 Oct 2020 04:08:42: 39000000 INFO @ Fri, 16 Oct 2020 04:08:46: 46000000 INFO @ Fri, 16 Oct 2020 04:08:46: 40000000 INFO @ Fri, 16 Oct 2020 04:08:46: 30000000 INFO @ Fri, 16 Oct 2020 04:08:50: 47000000 INFO @ Fri, 16 Oct 2020 04:08:51: 41000000 INFO @ Fri, 16 Oct 2020 04:08:52: 31000000 INFO @ Fri, 16 Oct 2020 04:08:55: 48000000 INFO @ Fri, 16 Oct 2020 04:08:56: 42000000 INFO @ Fri, 16 Oct 2020 04:08:57: 32000000 INFO @ Fri, 16 Oct 2020 04:09:00: 49000000 INFO @ Fri, 16 Oct 2020 04:09:01: 43000000 INFO @ Fri, 16 Oct 2020 04:09:02: 33000000 INFO @ Fri, 16 Oct 2020 04:09:04: 50000000 INFO @ Fri, 16 Oct 2020 04:09:05: 44000000 INFO @ Fri, 16 Oct 2020 04:09:07: 34000000 INFO @ Fri, 16 Oct 2020 04:09:09: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 04:09:09: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 04:09:09: #1 total tags in treatment: 50828201 INFO @ Fri, 16 Oct 2020 04:09:09: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 04:09:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 04:09:09: #1 tags after filtering in treatment: 50828060 INFO @ Fri, 16 Oct 2020 04:09:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 04:09:09: #1 finished! INFO @ Fri, 16 Oct 2020 04:09:09: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 04:09:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 04:09:10: 45000000 INFO @ Fri, 16 Oct 2020 04:09:12: 35000000 INFO @ Fri, 16 Oct 2020 04:09:15: 46000000 INFO @ Fri, 16 Oct 2020 04:09:17: #2 number of paired peaks: 113800 INFO @ Fri, 16 Oct 2020 04:09:17: start model_add_line... INFO @ Fri, 16 Oct 2020 04:09:17: 36000000 INFO @ Fri, 16 Oct 2020 04:09:18: start X-correlation... INFO @ Fri, 16 Oct 2020 04:09:18: end of X-cor INFO @ Fri, 16 Oct 2020 04:09:18: #2 finished! INFO @ Fri, 16 Oct 2020 04:09:18: #2 predicted fragment length is 227 bps INFO @ Fri, 16 Oct 2020 04:09:18: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 16 Oct 2020 04:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.05_model.r INFO @ Fri, 16 Oct 2020 04:09:18: #3 Call peaks... INFO @ Fri, 16 Oct 2020 04:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 04:09:19: 47000000 INFO @ Fri, 16 Oct 2020 04:09:22: 37000000 INFO @ Fri, 16 Oct 2020 04:09:24: 48000000 INFO @ Fri, 16 Oct 2020 04:09:28: 38000000 INFO @ Fri, 16 Oct 2020 04:09:29: 49000000 INFO @ Fri, 16 Oct 2020 04:09:33: 39000000 INFO @ Fri, 16 Oct 2020 04:09:33: 50000000 INFO @ Fri, 16 Oct 2020 04:09:38: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 04:09:38: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 04:09:38: #1 total tags in treatment: 50828201 INFO @ Fri, 16 Oct 2020 04:09:38: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 04:09:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 04:09:38: 40000000 INFO @ Fri, 16 Oct 2020 04:09:38: #1 tags after filtering in treatment: 50828060 INFO @ Fri, 16 Oct 2020 04:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 04:09:38: #1 finished! INFO @ Fri, 16 Oct 2020 04:09:38: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 04:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 04:09:43: 41000000 INFO @ Fri, 16 Oct 2020 04:09:46: #2 number of paired peaks: 113800 INFO @ Fri, 16 Oct 2020 04:09:46: start model_add_line... INFO @ Fri, 16 Oct 2020 04:09:47: start X-correlation... INFO @ Fri, 16 Oct 2020 04:09:47: end of X-cor INFO @ Fri, 16 Oct 2020 04:09:47: #2 finished! INFO @ Fri, 16 Oct 2020 04:09:47: #2 predicted fragment length is 227 bps INFO @ Fri, 16 Oct 2020 04:09:47: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 16 Oct 2020 04:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.10_model.r INFO @ Fri, 16 Oct 2020 04:09:47: #3 Call peaks... INFO @ Fri, 16 Oct 2020 04:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 04:09:48: 42000000 INFO @ Fri, 16 Oct 2020 04:09:53: 43000000 INFO @ Fri, 16 Oct 2020 04:09:58: 44000000 INFO @ Fri, 16 Oct 2020 04:10:03: 45000000 INFO @ Fri, 16 Oct 2020 04:10:09: 46000000 INFO @ Fri, 16 Oct 2020 04:10:14: 47000000 INFO @ Fri, 16 Oct 2020 04:10:19: 48000000 INFO @ Fri, 16 Oct 2020 04:10:24: 49000000 INFO @ Fri, 16 Oct 2020 04:10:29: 50000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 04:10:33: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 04:10:33: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 04:10:33: #1 total tags in treatment: 50828201 INFO @ Fri, 16 Oct 2020 04:10:33: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 04:10:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 04:10:34: #1 tags after filtering in treatment: 50828060 INFO @ Fri, 16 Oct 2020 04:10:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 04:10:34: #1 finished! INFO @ Fri, 16 Oct 2020 04:10:34: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 04:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 04:10:42: #2 number of paired peaks: 113800 INFO @ Fri, 16 Oct 2020 04:10:42: start model_add_line... INFO @ Fri, 16 Oct 2020 04:10:43: start X-correlation... INFO @ Fri, 16 Oct 2020 04:10:43: end of X-cor INFO @ Fri, 16 Oct 2020 04:10:43: #2 finished! INFO @ Fri, 16 Oct 2020 04:10:43: #2 predicted fragment length is 227 bps INFO @ Fri, 16 Oct 2020 04:10:43: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 16 Oct 2020 04:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.20_model.r INFO @ Fri, 16 Oct 2020 04:10:43: #3 Call peaks... INFO @ Fri, 16 Oct 2020 04:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 04:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 04:11:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 04:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.05_peaks.xls INFO @ Fri, 16 Oct 2020 04:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 04:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.05_summits.bed INFO @ Fri, 16 Oct 2020 04:12:38: Done! pass1 - making usageList (145 chroms): 6 millis pass2 - checking and writing primary data (40572 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 04:12:47: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 04:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.10_peaks.xls INFO @ Fri, 16 Oct 2020 04:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 04:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.10_summits.bed INFO @ Fri, 16 Oct 2020 04:13:10: Done! pass1 - making usageList (116 chroms): 4 millis pass2 - checking and writing primary data (24999 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 04:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.20_peaks.xls INFO @ Fri, 16 Oct 2020 04:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 04:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745104/ERX2745104.20_summits.bed INFO @ Fri, 16 Oct 2020 04:14:01: Done! pass1 - making usageList (79 chroms): 3 millis pass2 - checking and writing primary data (14921 records, 4 fields): 15 millis CompletedMACS2peakCalling