Job ID = 5790695 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:14:14 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 19,518,704 reads read : 19,518,704 reads written : 19,518,704 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:04 Multiseed full-index search: 00:06:10 19518704 reads; of these: 19518704 (100.00%) were unpaired; of these: 4360958 (22.34%) aligned 0 times 9659768 (49.49%) aligned exactly 1 time 5497978 (28.17%) aligned >1 times 77.66% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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_rmdupse_core] 2566659 / 15157746 = 0.1693 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 Apr 2020 06:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.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 Apr 2020 06:29:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:29:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:29:22: 1000000 INFO @ Wed, 22 Apr 2020 06:29:27: 2000000 INFO @ Wed, 22 Apr 2020 06:29:32: 3000000 INFO @ Wed, 22 Apr 2020 06:29:37: 4000000 INFO @ Wed, 22 Apr 2020 06:29:42: 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 @ Wed, 22 Apr 2020 06:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.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 Apr 2020 06:29:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:29:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:29:47: 6000000 INFO @ Wed, 22 Apr 2020 06:29:51: 1000000 INFO @ Wed, 22 Apr 2020 06:29:53: 7000000 INFO @ Wed, 22 Apr 2020 06:29:57: 2000000 INFO @ Wed, 22 Apr 2020 06:29:58: 8000000 INFO @ Wed, 22 Apr 2020 06:30:02: 3000000 INFO @ Wed, 22 Apr 2020 06:30:03: 9000000 INFO @ Wed, 22 Apr 2020 06:30:08: 4000000 INFO @ Wed, 22 Apr 2020 06:30:09: 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 @ Wed, 22 Apr 2020 06:30:13: 5000000 INFO @ Wed, 22 Apr 2020 06:30:14: 11000000 INFO @ Wed, 22 Apr 2020 06:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.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 Apr 2020 06:30:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:30:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:30:19: 6000000 INFO @ Wed, 22 Apr 2020 06:30:20: 12000000 INFO @ Wed, 22 Apr 2020 06:30:22: 1000000 INFO @ Wed, 22 Apr 2020 06:30:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:30:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:30:24: #1 total tags in treatment: 12591087 INFO @ Wed, 22 Apr 2020 06:30:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:30:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:30:24: #1 tags after filtering in treatment: 12590891 INFO @ Wed, 22 Apr 2020 06:30:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:30:24: #1 finished! INFO @ Wed, 22 Apr 2020 06:30:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:30:25: 7000000 INFO @ Wed, 22 Apr 2020 06:30:26: #2 number of paired peaks: 18975 INFO @ Wed, 22 Apr 2020 06:30:26: start model_add_line... INFO @ Wed, 22 Apr 2020 06:30:26: start X-correlation... INFO @ Wed, 22 Apr 2020 06:30:26: end of X-cor INFO @ Wed, 22 Apr 2020 06:30:26: #2 finished! INFO @ Wed, 22 Apr 2020 06:30:26: #2 predicted fragment length is 214 bps INFO @ Wed, 22 Apr 2020 06:30:26: #2 alternative fragment length(s) may be 214 bps INFO @ Wed, 22 Apr 2020 06:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.05_model.r INFO @ Wed, 22 Apr 2020 06:30:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:30:28: 2000000 INFO @ Wed, 22 Apr 2020 06:30:30: 8000000 INFO @ Wed, 22 Apr 2020 06:30:33: 3000000 INFO @ Wed, 22 Apr 2020 06:30:36: 9000000 INFO @ Wed, 22 Apr 2020 06:30:39: 4000000 INFO @ Wed, 22 Apr 2020 06:30:42: 10000000 INFO @ Wed, 22 Apr 2020 06:30:44: 5000000 INFO @ Wed, 22 Apr 2020 06:30:47: 11000000 INFO @ Wed, 22 Apr 2020 06:30:50: 6000000 INFO @ Wed, 22 Apr 2020 06:30:53: 12000000 INFO @ Wed, 22 Apr 2020 06:30:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:30:55: 7000000 INFO @ Wed, 22 Apr 2020 06:30:56: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:30:56: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:30:56: #1 total tags in treatment: 12591087 INFO @ Wed, 22 Apr 2020 06:30:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:30:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:30:56: #1 tags after filtering in treatment: 12590891 INFO @ Wed, 22 Apr 2020 06:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:30:56: #1 finished! INFO @ Wed, 22 Apr 2020 06:30:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:30:58: #2 number of paired peaks: 18975 INFO @ Wed, 22 Apr 2020 06:30:58: start model_add_line... INFO @ Wed, 22 Apr 2020 06:30:58: start X-correlation... INFO @ Wed, 22 Apr 2020 06:30:58: end of X-cor INFO @ Wed, 22 Apr 2020 06:30:58: #2 finished! INFO @ Wed, 22 Apr 2020 06:30:58: #2 predicted fragment length is 214 bps INFO @ Wed, 22 Apr 2020 06:30:58: #2 alternative fragment length(s) may be 214 bps INFO @ Wed, 22 Apr 2020 06:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.10_model.r INFO @ Wed, 22 Apr 2020 06:30:58: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:31:01: 8000000 INFO @ Wed, 22 Apr 2020 06:31:06: 9000000 INFO @ Wed, 22 Apr 2020 06:31:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:31:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:31:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.05_summits.bed INFO @ Wed, 22 Apr 2020 06:31:08: Done! INFO @ Wed, 22 Apr 2020 06:31:11: 10000000 pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (5844 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:31:16: 11000000 INFO @ Wed, 22 Apr 2020 06:31:21: 12000000 INFO @ Wed, 22 Apr 2020 06:31:24: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:31:24: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:31:24: #1 total tags in treatment: 12591087 INFO @ Wed, 22 Apr 2020 06:31:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 06:31:24: #1 tags after filtering in treatment: 12590891 INFO @ Wed, 22 Apr 2020 06:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:31:24: #1 finished! INFO @ Wed, 22 Apr 2020 06:31:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:31:26: #2 number of paired peaks: 18975 INFO @ Wed, 22 Apr 2020 06:31:26: start model_add_line... INFO @ Wed, 22 Apr 2020 06:31:26: start X-correlation... INFO @ Wed, 22 Apr 2020 06:31:26: end of X-cor INFO @ Wed, 22 Apr 2020 06:31:26: #2 finished! INFO @ Wed, 22 Apr 2020 06:31:26: #2 predicted fragment length is 214 bps INFO @ Wed, 22 Apr 2020 06:31:26: #2 alternative fragment length(s) may be 214 bps INFO @ Wed, 22 Apr 2020 06:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.20_model.r INFO @ Wed, 22 Apr 2020 06:31:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:31:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.10_summits.bed INFO @ Wed, 22 Apr 2020 06:31:41: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (2112 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:31:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761727/SRX5761727.20_summits.bed INFO @ Wed, 22 Apr 2020 06:32:09: Done! pass1 - making usageList (42 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。