Job ID = 5720843 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:08:10 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 ) 2020-04-15T17:11:10 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 : 34,449,585 reads read : 34,449,585 reads written : 34,449,585 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:33 34449585 reads; of these: 34449585 (100.00%) were unpaired; of these: 1470715 (4.27%) aligned 0 times 23977266 (69.60%) aligned exactly 1 time 9001604 (26.13%) aligned >1 times 95.73% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12345435 / 32978870 = 0.3743 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 @ Thu, 16 Apr 2020 02:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 02:31:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:31:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:31:59: 1000000 INFO @ Thu, 16 Apr 2020 02:32:06: 2000000 INFO @ Thu, 16 Apr 2020 02:32:12: 3000000 INFO @ Thu, 16 Apr 2020 02:32:19: 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 @ Thu, 16 Apr 2020 02:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 02:32:22: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:32:22: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:32:25: 5000000 INFO @ Thu, 16 Apr 2020 02:32:27: 1000000 INFO @ Thu, 16 Apr 2020 02:32:32: 6000000 INFO @ Thu, 16 Apr 2020 02:32:32: 2000000 INFO @ Thu, 16 Apr 2020 02:32:37: 3000000 INFO @ Thu, 16 Apr 2020 02:32:39: 7000000 INFO @ Thu, 16 Apr 2020 02:32:42: 4000000 INFO @ Thu, 16 Apr 2020 02:32:45: 8000000 INFO @ Thu, 16 Apr 2020 02:32:47: 5000000 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 @ Thu, 16 Apr 2020 02:32:52: 9000000 INFO @ Thu, 16 Apr 2020 02:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 02:32:52: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:32:52: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:32:52: 6000000 INFO @ Thu, 16 Apr 2020 02:32:57: 1000000 INFO @ Thu, 16 Apr 2020 02:32:58: 7000000 INFO @ Thu, 16 Apr 2020 02:32:58: 10000000 INFO @ Thu, 16 Apr 2020 02:33:02: 2000000 INFO @ Thu, 16 Apr 2020 02:33:03: 8000000 INFO @ Thu, 16 Apr 2020 02:33:05: 11000000 INFO @ Thu, 16 Apr 2020 02:33:08: 3000000 INFO @ Thu, 16 Apr 2020 02:33:08: 9000000 INFO @ Thu, 16 Apr 2020 02:33:12: 12000000 INFO @ Thu, 16 Apr 2020 02:33:13: 4000000 INFO @ Thu, 16 Apr 2020 02:33:13: 10000000 INFO @ Thu, 16 Apr 2020 02:33:18: 5000000 INFO @ Thu, 16 Apr 2020 02:33:18: 11000000 INFO @ Thu, 16 Apr 2020 02:33:18: 13000000 INFO @ Thu, 16 Apr 2020 02:33:23: 6000000 INFO @ Thu, 16 Apr 2020 02:33:23: 12000000 INFO @ Thu, 16 Apr 2020 02:33:24: 14000000 INFO @ Thu, 16 Apr 2020 02:33:28: 7000000 INFO @ Thu, 16 Apr 2020 02:33:28: 13000000 INFO @ Thu, 16 Apr 2020 02:33:30: 15000000 INFO @ Thu, 16 Apr 2020 02:33:33: 8000000 INFO @ Thu, 16 Apr 2020 02:33:33: 14000000 INFO @ Thu, 16 Apr 2020 02:33:36: 16000000 INFO @ Thu, 16 Apr 2020 02:33:38: 9000000 INFO @ Thu, 16 Apr 2020 02:33:38: 15000000 INFO @ Thu, 16 Apr 2020 02:33:43: 17000000 INFO @ Thu, 16 Apr 2020 02:33:43: 10000000 INFO @ Thu, 16 Apr 2020 02:33:43: 16000000 INFO @ Thu, 16 Apr 2020 02:33:48: 11000000 INFO @ Thu, 16 Apr 2020 02:33:48: 17000000 INFO @ Thu, 16 Apr 2020 02:33:49: 18000000 INFO @ Thu, 16 Apr 2020 02:33:53: 12000000 INFO @ Thu, 16 Apr 2020 02:33:54: 18000000 INFO @ Thu, 16 Apr 2020 02:33:55: 19000000 INFO @ Thu, 16 Apr 2020 02:33:59: 19000000 INFO @ Thu, 16 Apr 2020 02:33:59: 13000000 INFO @ Thu, 16 Apr 2020 02:34:02: 20000000 INFO @ Thu, 16 Apr 2020 02:34:04: 20000000 INFO @ Thu, 16 Apr 2020 02:34:04: 14000000 INFO @ Thu, 16 Apr 2020 02:34:05: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:34:05: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:34:05: #1 total tags in treatment: 20633435 INFO @ Thu, 16 Apr 2020 02:34:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:34:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:34:05: #1 tags after filtering in treatment: 20633435 INFO @ Thu, 16 Apr 2020 02:34:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:34:05: #1 finished! INFO @ Thu, 16 Apr 2020 02:34:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:34:07: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:34:07: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:34:07: #1 total tags in treatment: 20633435 INFO @ Thu, 16 Apr 2020 02:34:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:34:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:34:07: #1 tags after filtering in treatment: 20633435 INFO @ Thu, 16 Apr 2020 02:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:34:07: #1 finished! INFO @ Thu, 16 Apr 2020 02:34:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:34:07: #2 number of paired peaks: 5032 INFO @ Thu, 16 Apr 2020 02:34:07: start model_add_line... INFO @ Thu, 16 Apr 2020 02:34:08: start X-correlation... INFO @ Thu, 16 Apr 2020 02:34:08: end of X-cor INFO @ Thu, 16 Apr 2020 02:34:08: #2 finished! INFO @ Thu, 16 Apr 2020 02:34:08: #2 predicted fragment length is 243 bps INFO @ Thu, 16 Apr 2020 02:34:08: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 16 Apr 2020 02:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.05_model.r INFO @ Thu, 16 Apr 2020 02:34:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:34:09: 15000000 INFO @ Thu, 16 Apr 2020 02:34:09: #2 number of paired peaks: 5032 INFO @ Thu, 16 Apr 2020 02:34:09: start model_add_line... INFO @ Thu, 16 Apr 2020 02:34:09: start X-correlation... INFO @ Thu, 16 Apr 2020 02:34:09: end of X-cor INFO @ Thu, 16 Apr 2020 02:34:09: #2 finished! INFO @ Thu, 16 Apr 2020 02:34:09: #2 predicted fragment length is 243 bps INFO @ Thu, 16 Apr 2020 02:34:09: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 16 Apr 2020 02:34:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.10_model.r INFO @ Thu, 16 Apr 2020 02:34:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:34:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:34:13: 16000000 INFO @ Thu, 16 Apr 2020 02:34:18: 17000000 INFO @ Thu, 16 Apr 2020 02:34:23: 18000000 INFO @ Thu, 16 Apr 2020 02:34:28: 19000000 INFO @ Thu, 16 Apr 2020 02:34:33: 20000000 INFO @ Thu, 16 Apr 2020 02:34:36: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:34:36: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:34:36: #1 total tags in treatment: 20633435 INFO @ Thu, 16 Apr 2020 02:34:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:34:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:34:36: #1 tags after filtering in treatment: 20633435 INFO @ Thu, 16 Apr 2020 02:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:34:36: #1 finished! INFO @ Thu, 16 Apr 2020 02:34:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:34:38: #2 number of paired peaks: 5032 INFO @ Thu, 16 Apr 2020 02:34:38: start model_add_line... INFO @ Thu, 16 Apr 2020 02:34:38: start X-correlation... INFO @ Thu, 16 Apr 2020 02:34:38: end of X-cor INFO @ Thu, 16 Apr 2020 02:34:38: #2 finished! INFO @ Thu, 16 Apr 2020 02:34:38: #2 predicted fragment length is 243 bps INFO @ Thu, 16 Apr 2020 02:34:38: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 16 Apr 2020 02:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.20_model.r INFO @ Thu, 16 Apr 2020 02:34:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:35:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:35:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:35:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.10_summits.bed INFO @ Thu, 16 Apr 2020 02:35:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8865 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:35:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.05_summits.bed INFO @ Thu, 16 Apr 2020 02:35:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10392 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:36:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:36:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:36:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436036/SRX5436036.20_summits.bed INFO @ Thu, 16 Apr 2020 02:36:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6991 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。