Job ID = 10223562 SRX = ERX2745103 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T17:52:48 prefetch.2.10.7: 1) Downloading 'ERR2731878'... 2020-10-15T17:52:48 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T17:54:18 prefetch.2.10.7: HTTPS download succeed 2020-10-15T17:54:18 prefetch.2.10.7: 1) 'ERR2731878' was downloaded successfully Read 50327458 spots for ERR2731878/ERR2731878.sra Written 50327458 spots for ERR2731878/ERR2731878.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:29:28 50327458 reads; of these: 50327458 (100.00%) were unpaired; of these: 1597153 (3.17%) aligned 0 times 42997501 (85.44%) aligned exactly 1 time 5732804 (11.39%) aligned >1 times 96.83% overall alignment rate Time searching: 00:29:35 Overall time: 00:29:35 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] 12807694 / 48730305 = 0.2628 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 03:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.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 03:34:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 03:34:22: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 03:34:28: 1000000 INFO @ Fri, 16 Oct 2020 03:34:33: 2000000 INFO @ Fri, 16 Oct 2020 03:34:38: 3000000 INFO @ Fri, 16 Oct 2020 03:34:43: 4000000 INFO @ Fri, 16 Oct 2020 03:34:48: 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 03:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.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 03:34:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 03:34:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 03:34:53: 6000000 INFO @ Fri, 16 Oct 2020 03:34:58: 1000000 INFO @ Fri, 16 Oct 2020 03:34:59: 7000000 INFO @ Fri, 16 Oct 2020 03:35:04: 2000000 INFO @ Fri, 16 Oct 2020 03:35:05: 8000000 INFO @ Fri, 16 Oct 2020 03:35:10: 3000000 INFO @ Fri, 16 Oct 2020 03:35:11: 9000000 INFO @ Fri, 16 Oct 2020 03:35:16: 4000000 INFO @ Fri, 16 Oct 2020 03:35:17: 10000000 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 03:35:22: 5000000 INFO @ Fri, 16 Oct 2020 03:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.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 03:35:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 03:35:22: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 03:35:22: 11000000 INFO @ Fri, 16 Oct 2020 03:35:27: 6000000 INFO @ Fri, 16 Oct 2020 03:35:28: 12000000 INFO @ Fri, 16 Oct 2020 03:35:28: 1000000 INFO @ Fri, 16 Oct 2020 03:35:33: 7000000 INFO @ Fri, 16 Oct 2020 03:35:34: 13000000 INFO @ Fri, 16 Oct 2020 03:35:34: 2000000 INFO @ Fri, 16 Oct 2020 03:35:39: 8000000 INFO @ Fri, 16 Oct 2020 03:35:40: 14000000 INFO @ Fri, 16 Oct 2020 03:35:40: 3000000 INFO @ Fri, 16 Oct 2020 03:35:45: 9000000 INFO @ Fri, 16 Oct 2020 03:35:46: 15000000 INFO @ Fri, 16 Oct 2020 03:35:46: 4000000 INFO @ Fri, 16 Oct 2020 03:35:51: 10000000 INFO @ Fri, 16 Oct 2020 03:35:52: 16000000 INFO @ Fri, 16 Oct 2020 03:35:52: 5000000 INFO @ Fri, 16 Oct 2020 03:35:57: 11000000 INFO @ Fri, 16 Oct 2020 03:35:58: 17000000 INFO @ Fri, 16 Oct 2020 03:35:58: 6000000 INFO @ Fri, 16 Oct 2020 03:36:03: 12000000 INFO @ Fri, 16 Oct 2020 03:36:03: 18000000 INFO @ Fri, 16 Oct 2020 03:36:04: 7000000 INFO @ Fri, 16 Oct 2020 03:36:08: 13000000 INFO @ Fri, 16 Oct 2020 03:36:09: 19000000 INFO @ Fri, 16 Oct 2020 03:36:10: 8000000 INFO @ Fri, 16 Oct 2020 03:36:14: 14000000 INFO @ Fri, 16 Oct 2020 03:36:15: 20000000 INFO @ Fri, 16 Oct 2020 03:36:16: 9000000 INFO @ Fri, 16 Oct 2020 03:36:20: 15000000 INFO @ Fri, 16 Oct 2020 03:36:21: 21000000 INFO @ Fri, 16 Oct 2020 03:36:22: 10000000 INFO @ Fri, 16 Oct 2020 03:36:26: 16000000 INFO @ Fri, 16 Oct 2020 03:36:27: 22000000 INFO @ Fri, 16 Oct 2020 03:36:28: 11000000 INFO @ Fri, 16 Oct 2020 03:36:32: 17000000 INFO @ Fri, 16 Oct 2020 03:36:33: 23000000 INFO @ Fri, 16 Oct 2020 03:36:33: 12000000 INFO @ Fri, 16 Oct 2020 03:36:38: 18000000 INFO @ Fri, 16 Oct 2020 03:36:39: 24000000 INFO @ Fri, 16 Oct 2020 03:36:39: 13000000 INFO @ Fri, 16 Oct 2020 03:36:44: 19000000 INFO @ Fri, 16 Oct 2020 03:36:44: 25000000 INFO @ Fri, 16 Oct 2020 03:36:45: 14000000 INFO @ Fri, 16 Oct 2020 03:36:49: 20000000 INFO @ Fri, 16 Oct 2020 03:36:50: 26000000 INFO @ Fri, 16 Oct 2020 03:36:51: 15000000 INFO @ Fri, 16 Oct 2020 03:36:55: 21000000 INFO @ Fri, 16 Oct 2020 03:36:56: 27000000 INFO @ Fri, 16 Oct 2020 03:36:57: 16000000 INFO @ Fri, 16 Oct 2020 03:37:01: 22000000 INFO @ Fri, 16 Oct 2020 03:37:02: 28000000 INFO @ Fri, 16 Oct 2020 03:37:03: 17000000 INFO @ Fri, 16 Oct 2020 03:37:07: 23000000 INFO @ Fri, 16 Oct 2020 03:37:08: 29000000 INFO @ Fri, 16 Oct 2020 03:37:09: 18000000 INFO @ Fri, 16 Oct 2020 03:37:13: 24000000 INFO @ Fri, 16 Oct 2020 03:37:13: 30000000 INFO @ Fri, 16 Oct 2020 03:37:15: 19000000 INFO @ Fri, 16 Oct 2020 03:37:19: 25000000 INFO @ Fri, 16 Oct 2020 03:37:19: 31000000 INFO @ Fri, 16 Oct 2020 03:37:20: 20000000 INFO @ Fri, 16 Oct 2020 03:37:25: 26000000 INFO @ Fri, 16 Oct 2020 03:37:25: 32000000 INFO @ Fri, 16 Oct 2020 03:37:26: 21000000 INFO @ Fri, 16 Oct 2020 03:37:30: 27000000 INFO @ Fri, 16 Oct 2020 03:37:31: 33000000 INFO @ Fri, 16 Oct 2020 03:37:32: 22000000 INFO @ Fri, 16 Oct 2020 03:37:36: 28000000 INFO @ Fri, 16 Oct 2020 03:37:37: 34000000 INFO @ Fri, 16 Oct 2020 03:37:38: 23000000 INFO @ Fri, 16 Oct 2020 03:37:42: 29000000 INFO @ Fri, 16 Oct 2020 03:37:43: 35000000 INFO @ Fri, 16 Oct 2020 03:37:44: 24000000 INFO @ Fri, 16 Oct 2020 03:37:48: 30000000 INFO @ Fri, 16 Oct 2020 03:37:48: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 03:37:48: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 03:37:48: #1 total tags in treatment: 35922611 INFO @ Fri, 16 Oct 2020 03:37:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 03:37:48: #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 03:37:49: #1 tags after filtering in treatment: 35922426 INFO @ Fri, 16 Oct 2020 03:37:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 03:37:49: #1 finished! INFO @ Fri, 16 Oct 2020 03:37:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 03:37:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 03:37:50: 25000000 INFO @ Fri, 16 Oct 2020 03:37:53: 31000000 INFO @ Fri, 16 Oct 2020 03:37:55: #2 number of paired peaks: 111564 INFO @ Fri, 16 Oct 2020 03:37:55: start model_add_line... INFO @ Fri, 16 Oct 2020 03:37:56: start X-correlation... INFO @ Fri, 16 Oct 2020 03:37:56: end of X-cor INFO @ Fri, 16 Oct 2020 03:37:56: #2 finished! INFO @ Fri, 16 Oct 2020 03:37:56: #2 predicted fragment length is 225 bps INFO @ Fri, 16 Oct 2020 03:37:56: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 16 Oct 2020 03:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.05_model.r INFO @ Fri, 16 Oct 2020 03:37:56: #3 Call peaks... INFO @ Fri, 16 Oct 2020 03:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 03:37:56: 26000000 INFO @ Fri, 16 Oct 2020 03:37:59: 32000000 INFO @ Fri, 16 Oct 2020 03:38:02: 27000000 INFO @ Fri, 16 Oct 2020 03:38:05: 33000000 INFO @ Fri, 16 Oct 2020 03:38:07: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 03:38:11: 34000000 INFO @ Fri, 16 Oct 2020 03:38:13: 29000000 INFO @ Fri, 16 Oct 2020 03:38:16: 35000000 INFO @ Fri, 16 Oct 2020 03:38:19: 30000000 INFO @ Fri, 16 Oct 2020 03:38:22: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 03:38:22: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 03:38:22: #1 total tags in treatment: 35922611 INFO @ Fri, 16 Oct 2020 03:38:22: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 03:38:22: #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 03:38:23: #1 tags after filtering in treatment: 35922426 INFO @ Fri, 16 Oct 2020 03:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 03:38:23: #1 finished! INFO @ Fri, 16 Oct 2020 03:38:23: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 03:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 03:38:24: 31000000 INFO @ Fri, 16 Oct 2020 03:38:29: #2 number of paired peaks: 111564 INFO @ Fri, 16 Oct 2020 03:38:29: start model_add_line... INFO @ Fri, 16 Oct 2020 03:38:29: 32000000 INFO @ Fri, 16 Oct 2020 03:38:30: start X-correlation... INFO @ Fri, 16 Oct 2020 03:38:30: end of X-cor INFO @ Fri, 16 Oct 2020 03:38:30: #2 finished! INFO @ Fri, 16 Oct 2020 03:38:30: #2 predicted fragment length is 225 bps INFO @ Fri, 16 Oct 2020 03:38:30: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 16 Oct 2020 03:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.10_model.r INFO @ Fri, 16 Oct 2020 03:38:30: #3 Call peaks... INFO @ Fri, 16 Oct 2020 03:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 03:38:34: 33000000 INFO @ Fri, 16 Oct 2020 03:38:40: 34000000 INFO @ Fri, 16 Oct 2020 03:38:45: 35000000 INFO @ Fri, 16 Oct 2020 03:38:50: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 03:38:50: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 03:38:50: #1 total tags in treatment: 35922611 INFO @ Fri, 16 Oct 2020 03:38:50: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 03:38:50: #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 03:38:51: #1 tags after filtering in treatment: 35922426 INFO @ Fri, 16 Oct 2020 03:38:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 03:38:51: #1 finished! INFO @ Fri, 16 Oct 2020 03:38:51: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 03:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 03:38:57: #2 number of paired peaks: 111564 INFO @ Fri, 16 Oct 2020 03:38:57: start model_add_line... INFO @ Fri, 16 Oct 2020 03:38:57: start X-correlation... INFO @ Fri, 16 Oct 2020 03:38:57: end of X-cor INFO @ Fri, 16 Oct 2020 03:38:57: #2 finished! INFO @ Fri, 16 Oct 2020 03:38:57: #2 predicted fragment length is 225 bps INFO @ Fri, 16 Oct 2020 03:38:57: #2 alternative fragment length(s) may be 225 bps INFO @ Fri, 16 Oct 2020 03:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.20_model.r INFO @ Fri, 16 Oct 2020 03:38:57: #3 Call peaks... INFO @ Fri, 16 Oct 2020 03:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 03:39:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 03:39:55: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 03:40:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.05_peaks.xls INFO @ Fri, 16 Oct 2020 03:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 03:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.05_summits.bed INFO @ Fri, 16 Oct 2020 03:40:08: Done! pass1 - making usageList (132 chroms): 5 millis pass2 - checking and writing primary data (32897 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 03:40:23: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 03:40:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.10_peaks.xls INFO @ Fri, 16 Oct 2020 03:40:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 03:40:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.10_summits.bed INFO @ Fri, 16 Oct 2020 03:40:42: Done! pass1 - making usageList (97 chroms): 3 millis pass2 - checking and writing primary data (19930 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 03:41:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.20_peaks.xls INFO @ Fri, 16 Oct 2020 03:41:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 03:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745103/ERX2745103.20_summits.bed INFO @ Fri, 16 Oct 2020 03:41:11: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (11076 records, 4 fields): 13 millis CompletedMACS2peakCalling