Job ID = 5790655 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:09:23 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 : 35,733,583 reads read : 71,467,166 reads written : 35,733,583 reads 0-length : 35,733,583 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:29:29 35733583 reads; of these: 35733583 (100.00%) were unpaired; of these: 3010266 (8.42%) aligned 0 times 23828857 (66.68%) aligned exactly 1 time 8894460 (24.89%) aligned >1 times 91.58% overall alignment rate Time searching: 00:29:33 Overall time: 00:29:33 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 16 files... [bam_rmdupse_core] 2511256 / 32723317 = 0.0767 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 05:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.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 05:48:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:48:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:48:35: 1000000 INFO @ Wed, 22 Apr 2020 05:48:42: 2000000 INFO @ Wed, 22 Apr 2020 05:48:49: 3000000 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 05:48:57: 4000000 INFO @ Wed, 22 Apr 2020 05:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.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 05:48:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:48:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:49:05: 5000000 INFO @ Wed, 22 Apr 2020 05:49:05: 1000000 INFO @ Wed, 22 Apr 2020 05:49:13: 6000000 INFO @ Wed, 22 Apr 2020 05:49:13: 2000000 INFO @ Wed, 22 Apr 2020 05:49:21: 3000000 INFO @ Wed, 22 Apr 2020 05:49:21: 7000000 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 05:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.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 05:49:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:49:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:49:29: 4000000 INFO @ Wed, 22 Apr 2020 05:49:29: 8000000 INFO @ Wed, 22 Apr 2020 05:49:36: 5000000 INFO @ Wed, 22 Apr 2020 05:49:37: 1000000 INFO @ Wed, 22 Apr 2020 05:49:38: 9000000 INFO @ Wed, 22 Apr 2020 05:49:44: 6000000 INFO @ Wed, 22 Apr 2020 05:49:45: 2000000 INFO @ Wed, 22 Apr 2020 05:49:46: 10000000 INFO @ Wed, 22 Apr 2020 05:49:52: 7000000 INFO @ Wed, 22 Apr 2020 05:49:53: 3000000 INFO @ Wed, 22 Apr 2020 05:49:54: 11000000 INFO @ Wed, 22 Apr 2020 05:50:00: 8000000 INFO @ Wed, 22 Apr 2020 05:50:01: 4000000 INFO @ Wed, 22 Apr 2020 05:50:02: 12000000 INFO @ Wed, 22 Apr 2020 05:50:07: 9000000 INFO @ Wed, 22 Apr 2020 05:50:08: 5000000 INFO @ Wed, 22 Apr 2020 05:50:10: 13000000 INFO @ Wed, 22 Apr 2020 05:50:15: 10000000 INFO @ Wed, 22 Apr 2020 05:50:16: 6000000 INFO @ Wed, 22 Apr 2020 05:50:19: 14000000 INFO @ Wed, 22 Apr 2020 05:50:22: 11000000 INFO @ Wed, 22 Apr 2020 05:50:23: 7000000 INFO @ Wed, 22 Apr 2020 05:50:27: 15000000 INFO @ Wed, 22 Apr 2020 05:50:30: 12000000 INFO @ Wed, 22 Apr 2020 05:50:31: 8000000 INFO @ Wed, 22 Apr 2020 05:50:35: 16000000 INFO @ Wed, 22 Apr 2020 05:50:37: 13000000 INFO @ Wed, 22 Apr 2020 05:50:38: 9000000 INFO @ Wed, 22 Apr 2020 05:50:43: 17000000 INFO @ Wed, 22 Apr 2020 05:50:45: 14000000 INFO @ Wed, 22 Apr 2020 05:50:46: 10000000 INFO @ Wed, 22 Apr 2020 05:50:51: 18000000 INFO @ Wed, 22 Apr 2020 05:50:52: 15000000 INFO @ Wed, 22 Apr 2020 05:50:53: 11000000 INFO @ Wed, 22 Apr 2020 05:50:59: 19000000 INFO @ Wed, 22 Apr 2020 05:51:00: 16000000 INFO @ Wed, 22 Apr 2020 05:51:00: 12000000 INFO @ Wed, 22 Apr 2020 05:51:07: 17000000 INFO @ Wed, 22 Apr 2020 05:51:07: 20000000 INFO @ Wed, 22 Apr 2020 05:51:08: 13000000 INFO @ Wed, 22 Apr 2020 05:51:14: 18000000 INFO @ Wed, 22 Apr 2020 05:51:15: 21000000 INFO @ Wed, 22 Apr 2020 05:51:15: 14000000 INFO @ Wed, 22 Apr 2020 05:51:22: 19000000 INFO @ Wed, 22 Apr 2020 05:51:22: 15000000 INFO @ Wed, 22 Apr 2020 05:51:23: 22000000 INFO @ Wed, 22 Apr 2020 05:51:29: 20000000 INFO @ Wed, 22 Apr 2020 05:51:30: 16000000 INFO @ Wed, 22 Apr 2020 05:51:31: 23000000 INFO @ Wed, 22 Apr 2020 05:51:36: 21000000 INFO @ Wed, 22 Apr 2020 05:51:37: 17000000 INFO @ Wed, 22 Apr 2020 05:51:38: 24000000 INFO @ Wed, 22 Apr 2020 05:51:44: 22000000 INFO @ Wed, 22 Apr 2020 05:51:45: 18000000 INFO @ Wed, 22 Apr 2020 05:51:46: 25000000 INFO @ Wed, 22 Apr 2020 05:51:51: 23000000 INFO @ Wed, 22 Apr 2020 05:51:52: 19000000 INFO @ Wed, 22 Apr 2020 05:51:54: 26000000 INFO @ Wed, 22 Apr 2020 05:51:59: 24000000 INFO @ Wed, 22 Apr 2020 05:52:00: 20000000 INFO @ Wed, 22 Apr 2020 05:52:02: 27000000 INFO @ Wed, 22 Apr 2020 05:52:07: 25000000 INFO @ Wed, 22 Apr 2020 05:52:08: 21000000 INFO @ Wed, 22 Apr 2020 05:52:11: 28000000 INFO @ Wed, 22 Apr 2020 05:52:14: 26000000 INFO @ Wed, 22 Apr 2020 05:52:15: 22000000 INFO @ Wed, 22 Apr 2020 05:52:19: 29000000 INFO @ Wed, 22 Apr 2020 05:52:22: 27000000 INFO @ Wed, 22 Apr 2020 05:52:23: 23000000 INFO @ Wed, 22 Apr 2020 05:52:27: 30000000 INFO @ Wed, 22 Apr 2020 05:52:29: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 05:52:29: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 05:52:29: #1 total tags in treatment: 30212061 INFO @ Wed, 22 Apr 2020 05:52:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:52:29: #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 05:52:30: #1 tags after filtering in treatment: 30211959 INFO @ Wed, 22 Apr 2020 05:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:52:30: #1 finished! INFO @ Wed, 22 Apr 2020 05:52:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:52:30: 28000000 INFO @ Wed, 22 Apr 2020 05:52:31: 24000000 INFO @ Wed, 22 Apr 2020 05:52:33: #2 number of paired peaks: 17797 INFO @ Wed, 22 Apr 2020 05:52:33: start model_add_line... INFO @ Wed, 22 Apr 2020 05:52:33: start X-correlation... INFO @ Wed, 22 Apr 2020 05:52:33: end of X-cor INFO @ Wed, 22 Apr 2020 05:52:33: #2 finished! INFO @ Wed, 22 Apr 2020 05:52:33: #2 predicted fragment length is 134 bps INFO @ Wed, 22 Apr 2020 05:52:33: #2 alternative fragment length(s) may be 134 bps INFO @ Wed, 22 Apr 2020 05:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.05_model.r INFO @ Wed, 22 Apr 2020 05:52:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:52:37: 29000000 INFO @ Wed, 22 Apr 2020 05:52:38: 25000000 INFO @ Wed, 22 Apr 2020 05:52:44: 30000000 INFO @ Wed, 22 Apr 2020 05:52:45: 26000000 INFO @ Wed, 22 Apr 2020 05:52:46: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 05:52:46: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 05:52:46: #1 total tags in treatment: 30212061 INFO @ Wed, 22 Apr 2020 05:52:46: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:52:46: #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 05:52:46: #1 tags after filtering in treatment: 30211959 INFO @ Wed, 22 Apr 2020 05:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:52:46: #1 finished! INFO @ Wed, 22 Apr 2020 05:52:46: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:52:49: #2 number of paired peaks: 17797 INFO @ Wed, 22 Apr 2020 05:52:49: start model_add_line... INFO @ Wed, 22 Apr 2020 05:52:49: start X-correlation... INFO @ Wed, 22 Apr 2020 05:52:50: end of X-cor INFO @ Wed, 22 Apr 2020 05:52:50: #2 finished! INFO @ Wed, 22 Apr 2020 05:52:50: #2 predicted fragment length is 134 bps INFO @ Wed, 22 Apr 2020 05:52:50: #2 alternative fragment length(s) may be 134 bps INFO @ Wed, 22 Apr 2020 05:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.10_model.r INFO @ Wed, 22 Apr 2020 05:52:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:52:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:52:51: 27000000 INFO @ Wed, 22 Apr 2020 05:52:59: 28000000 INFO @ Wed, 22 Apr 2020 05:53:07: 29000000 INFO @ Wed, 22 Apr 2020 05:53:13: 30000000 INFO @ Wed, 22 Apr 2020 05:53:14: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 05:53:14: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 05:53:14: #1 total tags in treatment: 30212061 INFO @ Wed, 22 Apr 2020 05:53:14: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:53:14: #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 05:53:15: #1 tags after filtering in treatment: 30211959 INFO @ Wed, 22 Apr 2020 05:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:53:15: #1 finished! INFO @ Wed, 22 Apr 2020 05:53:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:53:18: #2 number of paired peaks: 17797 INFO @ Wed, 22 Apr 2020 05:53:18: start model_add_line... INFO @ Wed, 22 Apr 2020 05:53:18: start X-correlation... INFO @ Wed, 22 Apr 2020 05:53:18: end of X-cor INFO @ Wed, 22 Apr 2020 05:53:18: #2 finished! INFO @ Wed, 22 Apr 2020 05:53:18: #2 predicted fragment length is 134 bps INFO @ Wed, 22 Apr 2020 05:53:18: #2 alternative fragment length(s) may be 134 bps INFO @ Wed, 22 Apr 2020 05:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.20_model.r INFO @ Wed, 22 Apr 2020 05:53:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:53:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:53:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.05_summits.bed INFO @ Wed, 22 Apr 2020 05:54:15: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (6209 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:54:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 05:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.10_summits.bed INFO @ Wed, 22 Apr 2020 05:54:31: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (2145 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433266/SRX5433266.20_summits.bed INFO @ Wed, 22 Apr 2020 05:55:00: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (761 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。