Job ID = 5790713 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:24:06 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 ) 2020-04-21T21:29:03 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 ) 2020-04-21T21:29:03 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 : 25,363,840 reads read : 25,363,840 reads written : 25,363,840 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:03 25363840 reads; of these: 25363840 (100.00%) were unpaired; of these: 7178778 (28.30%) aligned 0 times 11941604 (47.08%) aligned exactly 1 time 6243458 (24.62%) aligned >1 times 71.70% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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 8 files... [bam_rmdupse_core] 4879143 / 18185062 = 0.2683 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 06:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.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 06:48:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:48:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:48:44: 1000000 INFO @ Wed, 22 Apr 2020 06:48:50: 2000000 INFO @ Wed, 22 Apr 2020 06:48:56: 3000000 INFO @ Wed, 22 Apr 2020 06:49:02: 4000000 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 06:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.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 06:49:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:49:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:49:08: 5000000 INFO @ Wed, 22 Apr 2020 06:49:14: 1000000 INFO @ Wed, 22 Apr 2020 06:49:15: 6000000 INFO @ Wed, 22 Apr 2020 06:49:20: 2000000 INFO @ Wed, 22 Apr 2020 06:49:21: 7000000 INFO @ Wed, 22 Apr 2020 06:49:26: 3000000 INFO @ Wed, 22 Apr 2020 06:49:27: 8000000 INFO @ Wed, 22 Apr 2020 06:49:33: 4000000 INFO @ Wed, 22 Apr 2020 06:49:33: 9000000 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 06:49:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.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 06:49:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:49:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:49:39: 5000000 INFO @ Wed, 22 Apr 2020 06:49:40: 10000000 INFO @ Wed, 22 Apr 2020 06:49:43: 1000000 INFO @ Wed, 22 Apr 2020 06:49:46: 6000000 INFO @ Wed, 22 Apr 2020 06:49:47: 11000000 INFO @ Wed, 22 Apr 2020 06:49:49: 2000000 INFO @ Wed, 22 Apr 2020 06:49:53: 7000000 INFO @ Wed, 22 Apr 2020 06:49:53: 12000000 INFO @ Wed, 22 Apr 2020 06:49:55: 3000000 INFO @ Wed, 22 Apr 2020 06:49:59: 8000000 INFO @ Wed, 22 Apr 2020 06:50:00: 13000000 INFO @ Wed, 22 Apr 2020 06:50:01: 4000000 INFO @ Wed, 22 Apr 2020 06:50:03: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:50:03: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:50:03: #1 total tags in treatment: 13305919 INFO @ Wed, 22 Apr 2020 06:50:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:50:03: #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 06:50:03: #1 tags after filtering in treatment: 13305752 INFO @ Wed, 22 Apr 2020 06:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:50:03: #1 finished! INFO @ Wed, 22 Apr 2020 06:50:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:50:05: #2 number of paired peaks: 45234 INFO @ Wed, 22 Apr 2020 06:50:05: start model_add_line... INFO @ Wed, 22 Apr 2020 06:50:05: start X-correlation... INFO @ Wed, 22 Apr 2020 06:50:05: end of X-cor INFO @ Wed, 22 Apr 2020 06:50:05: #2 finished! INFO @ Wed, 22 Apr 2020 06:50:05: #2 predicted fragment length is 191 bps INFO @ Wed, 22 Apr 2020 06:50:05: #2 alternative fragment length(s) may be 191 bps INFO @ Wed, 22 Apr 2020 06:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.05_model.r INFO @ Wed, 22 Apr 2020 06:50:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:50:06: 9000000 INFO @ Wed, 22 Apr 2020 06:50:07: 5000000 INFO @ Wed, 22 Apr 2020 06:50:13: 10000000 INFO @ Wed, 22 Apr 2020 06:50:13: 6000000 INFO @ Wed, 22 Apr 2020 06:50:19: 7000000 INFO @ Wed, 22 Apr 2020 06:50:19: 11000000 INFO @ Wed, 22 Apr 2020 06:50:25: 8000000 INFO @ Wed, 22 Apr 2020 06:50:26: 12000000 INFO @ Wed, 22 Apr 2020 06:50:31: 9000000 INFO @ Wed, 22 Apr 2020 06:50:32: 13000000 INFO @ Wed, 22 Apr 2020 06:50:34: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:50:34: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:50:34: #1 total tags in treatment: 13305919 INFO @ Wed, 22 Apr 2020 06:50:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:50:34: #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 06:50:34: #1 tags after filtering in treatment: 13305752 INFO @ Wed, 22 Apr 2020 06:50:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:50:34: #1 finished! INFO @ Wed, 22 Apr 2020 06:50:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:50:36: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:50:36: 10000000 INFO @ Wed, 22 Apr 2020 06:50:37: #2 number of paired peaks: 45234 INFO @ Wed, 22 Apr 2020 06:50:37: start model_add_line... INFO @ Wed, 22 Apr 2020 06:50:37: start X-correlation... INFO @ Wed, 22 Apr 2020 06:50:37: end of X-cor INFO @ Wed, 22 Apr 2020 06:50:37: #2 finished! INFO @ Wed, 22 Apr 2020 06:50:37: #2 predicted fragment length is 191 bps INFO @ Wed, 22 Apr 2020 06:50:37: #2 alternative fragment length(s) may be 191 bps INFO @ Wed, 22 Apr 2020 06:50:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.10_model.r INFO @ Wed, 22 Apr 2020 06:50:37: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:50:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:50:42: 11000000 INFO @ Wed, 22 Apr 2020 06:50:47: 12000000 INFO @ Wed, 22 Apr 2020 06:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.05_summits.bed INFO @ Wed, 22 Apr 2020 06:50:51: Done! pass1 - making usageList (128 chroms): 3 millis pass2 - checking and writing primary data (21319 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:50:52: 13000000 INFO @ Wed, 22 Apr 2020 06:50:54: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:50:54: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:50:54: #1 total tags in treatment: 13305919 INFO @ Wed, 22 Apr 2020 06:50:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:50:54: #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 06:50:54: #1 tags after filtering in treatment: 13305752 INFO @ Wed, 22 Apr 2020 06:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:50:54: #1 finished! INFO @ Wed, 22 Apr 2020 06:50:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:50:57: #2 number of paired peaks: 45234 INFO @ Wed, 22 Apr 2020 06:50:57: start model_add_line... INFO @ Wed, 22 Apr 2020 06:50:57: start X-correlation... INFO @ Wed, 22 Apr 2020 06:50:57: end of X-cor INFO @ Wed, 22 Apr 2020 06:50:57: #2 finished! INFO @ Wed, 22 Apr 2020 06:50:57: #2 predicted fragment length is 191 bps INFO @ Wed, 22 Apr 2020 06:50:57: #2 alternative fragment length(s) may be 191 bps INFO @ Wed, 22 Apr 2020 06:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.20_model.r INFO @ Wed, 22 Apr 2020 06:50:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:51:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:51:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:51:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.10_summits.bed INFO @ Wed, 22 Apr 2020 06:51:24: Done! pass1 - making usageList (82 chroms): 2 millis pass2 - checking and writing primary data (7027 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:51:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761743/SRX5761743.20_summits.bed INFO @ Wed, 22 Apr 2020 06:51:43: Done! pass1 - making usageList (47 chroms): 0 millis pass2 - checking and writing primary data (609 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。