Job ID = 10223654 SRX = ERX2745129 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-15T20:04:58 prefetch.2.10.7: 1) Downloading 'ERR2731904'... 2020-10-15T20:04:58 prefetch.2.10.7: Downloading via HTTPS... 2020-10-15T20:06:17 prefetch.2.10.7: HTTPS download succeed 2020-10-15T20:06:17 prefetch.2.10.7: 1) 'ERR2731904' was downloaded successfully Read 43573292 spots for ERR2731904/ERR2731904.sra Written 43573292 spots for ERR2731904/ERR2731904.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: 00:00:01 Multiseed full-index search: 00:19:39 43573292 reads; of these: 43573292 (100.00%) were unpaired; of these: 1880131 (4.31%) aligned 0 times 36819017 (84.50%) aligned exactly 1 time 4874144 (11.19%) aligned >1 times 95.69% overall alignment rate Time searching: 00:19:41 Overall time: 00:19:41 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] 16415084 / 41693161 = 0.3937 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 05:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.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 05:34:42: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:34:42: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:34:47: 1000000 INFO @ Fri, 16 Oct 2020 05:34:52: 2000000 INFO @ Fri, 16 Oct 2020 05:34:57: 3000000 INFO @ Fri, 16 Oct 2020 05:35:02: 4000000 INFO @ Fri, 16 Oct 2020 05:35:08: 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 05:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.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 05:35:11: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:35:11: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:35:13: 6000000 INFO @ Fri, 16 Oct 2020 05:35:17: 1000000 INFO @ Fri, 16 Oct 2020 05:35:19: 7000000 INFO @ Fri, 16 Oct 2020 05:35:22: 2000000 INFO @ Fri, 16 Oct 2020 05:35:24: 8000000 INFO @ Fri, 16 Oct 2020 05:35:28: 3000000 INFO @ Fri, 16 Oct 2020 05:35:30: 9000000 INFO @ Fri, 16 Oct 2020 05:35:34: 4000000 INFO @ Fri, 16 Oct 2020 05:35:36: 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 05:35:39: 5000000 INFO @ Fri, 16 Oct 2020 05:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.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 05:35:41: #1 read tag files... INFO @ Fri, 16 Oct 2020 05:35:41: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 05:35:42: 11000000 INFO @ Fri, 16 Oct 2020 05:35:45: 6000000 INFO @ Fri, 16 Oct 2020 05:35:47: 1000000 INFO @ Fri, 16 Oct 2020 05:35:47: 12000000 INFO @ Fri, 16 Oct 2020 05:35:51: 7000000 INFO @ Fri, 16 Oct 2020 05:35:53: 2000000 INFO @ Fri, 16 Oct 2020 05:35:53: 13000000 INFO @ Fri, 16 Oct 2020 05:35:57: 8000000 INFO @ Fri, 16 Oct 2020 05:35:59: 3000000 INFO @ Fri, 16 Oct 2020 05:35:59: 14000000 INFO @ Fri, 16 Oct 2020 05:36:02: 9000000 INFO @ Fri, 16 Oct 2020 05:36:04: 4000000 INFO @ Fri, 16 Oct 2020 05:36:05: 15000000 INFO @ Fri, 16 Oct 2020 05:36:08: 10000000 INFO @ Fri, 16 Oct 2020 05:36:10: 5000000 INFO @ Fri, 16 Oct 2020 05:36:10: 16000000 INFO @ Fri, 16 Oct 2020 05:36:14: 11000000 INFO @ Fri, 16 Oct 2020 05:36:16: 6000000 INFO @ Fri, 16 Oct 2020 05:36:16: 17000000 INFO @ Fri, 16 Oct 2020 05:36:19: 12000000 INFO @ Fri, 16 Oct 2020 05:36:22: 7000000 INFO @ Fri, 16 Oct 2020 05:36:22: 18000000 INFO @ Fri, 16 Oct 2020 05:36:25: 13000000 INFO @ Fri, 16 Oct 2020 05:36:27: 8000000 INFO @ Fri, 16 Oct 2020 05:36:28: 19000000 INFO @ Fri, 16 Oct 2020 05:36:31: 14000000 INFO @ Fri, 16 Oct 2020 05:36:33: 9000000 INFO @ Fri, 16 Oct 2020 05:36:34: 20000000 INFO @ Fri, 16 Oct 2020 05:36:37: 15000000 INFO @ Fri, 16 Oct 2020 05:36:39: 10000000 INFO @ Fri, 16 Oct 2020 05:36:39: 21000000 INFO @ Fri, 16 Oct 2020 05:36:42: 16000000 INFO @ Fri, 16 Oct 2020 05:36:45: 11000000 INFO @ Fri, 16 Oct 2020 05:36:45: 22000000 INFO @ Fri, 16 Oct 2020 05:36:48: 17000000 INFO @ Fri, 16 Oct 2020 05:36:51: 12000000 INFO @ Fri, 16 Oct 2020 05:36:51: 23000000 INFO @ Fri, 16 Oct 2020 05:36:54: 18000000 INFO @ Fri, 16 Oct 2020 05:36:56: 13000000 INFO @ Fri, 16 Oct 2020 05:36:57: 24000000 INFO @ Fri, 16 Oct 2020 05:36:59: 19000000 INFO @ Fri, 16 Oct 2020 05:37:02: 14000000 INFO @ Fri, 16 Oct 2020 05:37:03: 25000000 INFO @ Fri, 16 Oct 2020 05:37:05: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:37:05: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:37:05: #1 total tags in treatment: 25278077 INFO @ Fri, 16 Oct 2020 05:37:05: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:37:05: #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 05:37:05: #1 tags after filtering in treatment: 25277840 INFO @ Fri, 16 Oct 2020 05:37:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:37:05: #1 finished! INFO @ Fri, 16 Oct 2020 05:37:05: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:37:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:37:05: 20000000 INFO @ Fri, 16 Oct 2020 05:37:08: 15000000 INFO @ Fri, 16 Oct 2020 05:37:08: #2 number of paired peaks: 34216 INFO @ Fri, 16 Oct 2020 05:37:08: start model_add_line... INFO @ Fri, 16 Oct 2020 05:37:09: start X-correlation... INFO @ Fri, 16 Oct 2020 05:37:09: end of X-cor INFO @ Fri, 16 Oct 2020 05:37:09: #2 finished! INFO @ Fri, 16 Oct 2020 05:37:09: #2 predicted fragment length is 225 bps INFO @ Fri, 16 Oct 2020 05:37:09: #2 alternative fragment length(s) may be 4,225 bps INFO @ Fri, 16 Oct 2020 05:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.05_model.r INFO @ Fri, 16 Oct 2020 05:37:09: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:37:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:37:11: 21000000 INFO @ Fri, 16 Oct 2020 05:37:14: 16000000 INFO @ Fri, 16 Oct 2020 05:37:17: 22000000 INFO @ Fri, 16 Oct 2020 05:37:19: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 05:37:22: 23000000 INFO @ Fri, 16 Oct 2020 05:37:25: 18000000 INFO @ Fri, 16 Oct 2020 05:37:28: 24000000 INFO @ Fri, 16 Oct 2020 05:37:31: 19000000 INFO @ Fri, 16 Oct 2020 05:37:34: 25000000 INFO @ Fri, 16 Oct 2020 05:37:36: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:37:36: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:37:36: #1 total tags in treatment: 25278077 INFO @ Fri, 16 Oct 2020 05:37:36: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:37:36: #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 05:37:36: #1 tags after filtering in treatment: 25277840 INFO @ Fri, 16 Oct 2020 05:37:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:37:36: #1 finished! INFO @ Fri, 16 Oct 2020 05:37:36: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:37:37: 20000000 INFO @ Fri, 16 Oct 2020 05:37:39: #2 number of paired peaks: 34216 INFO @ Fri, 16 Oct 2020 05:37:39: start model_add_line... INFO @ Fri, 16 Oct 2020 05:37:40: start X-correlation... INFO @ Fri, 16 Oct 2020 05:37:40: end of X-cor INFO @ Fri, 16 Oct 2020 05:37:40: #2 finished! INFO @ Fri, 16 Oct 2020 05:37:40: #2 predicted fragment length is 225 bps INFO @ Fri, 16 Oct 2020 05:37:40: #2 alternative fragment length(s) may be 4,225 bps INFO @ Fri, 16 Oct 2020 05:37:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.10_model.r INFO @ Fri, 16 Oct 2020 05:37:40: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:37:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:37:42: 21000000 INFO @ Fri, 16 Oct 2020 05:37:47: 22000000 INFO @ Fri, 16 Oct 2020 05:37:53: 23000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 05:37:58: 24000000 INFO @ Fri, 16 Oct 2020 05:38:03: 25000000 INFO @ Fri, 16 Oct 2020 05:38:05: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 05:38:05: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 05:38:05: #1 total tags in treatment: 25278077 INFO @ Fri, 16 Oct 2020 05:38:05: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 05:38:05: #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 05:38:05: #1 tags after filtering in treatment: 25277840 INFO @ Fri, 16 Oct 2020 05:38:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 05:38:05: #1 finished! INFO @ Fri, 16 Oct 2020 05:38:05: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 05:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 05:38:09: #2 number of paired peaks: 34216 INFO @ Fri, 16 Oct 2020 05:38:09: start model_add_line... INFO @ Fri, 16 Oct 2020 05:38:09: start X-correlation... INFO @ Fri, 16 Oct 2020 05:38:09: end of X-cor INFO @ Fri, 16 Oct 2020 05:38:09: #2 finished! INFO @ Fri, 16 Oct 2020 05:38:09: #2 predicted fragment length is 225 bps INFO @ Fri, 16 Oct 2020 05:38:09: #2 alternative fragment length(s) may be 4,225 bps INFO @ Fri, 16 Oct 2020 05:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.20_model.r INFO @ Fri, 16 Oct 2020 05:38:09: #3 Call peaks... INFO @ Fri, 16 Oct 2020 05:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 05:38:15: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:38:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.05_peaks.xls INFO @ Fri, 16 Oct 2020 05:38:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:38:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.05_summits.bed INFO @ Fri, 16 Oct 2020 05:38:49: Done! pass1 - making usageList (129 chroms): 4 millis pass2 - checking and writing primary data (23136 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:39:13: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 05:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.10_peaks.xls INFO @ Fri, 16 Oct 2020 05:39:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:39:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.10_summits.bed INFO @ Fri, 16 Oct 2020 05:39:19: Done! pass1 - making usageList (119 chroms): 4 millis pass2 - checking and writing primary data (21103 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 05:39:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.20_peaks.xls INFO @ Fri, 16 Oct 2020 05:39:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 05:39:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2745129/ERX2745129.20_summits.bed INFO @ Fri, 16 Oct 2020 05:39:48: Done! pass1 - making usageList (102 chroms): 3 millis pass2 - checking and writing primary data (19097 records, 4 fields): 21 millis CompletedMACS2peakCalling