Job ID = 5720315 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:05:21 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 ) 2020-04-15T14:05:37 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 : 14,232,699 reads read : 14,232,699 reads written : 14,232,699 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: 00:01:54 14232699 reads; of these: 14232699 (100.00%) were unpaired; of these: 6770154 (47.57%) aligned 0 times 6366256 (44.73%) aligned exactly 1 time 1096289 (7.70%) aligned >1 times 52.43% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1193306 / 7462545 = 0.1599 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, 15 Apr 2020 23:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:16:24: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:16:24: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:16:29: 1000000 INFO @ Wed, 15 Apr 2020 23:16:34: 2000000 INFO @ Wed, 15 Apr 2020 23:16:39: 3000000 INFO @ Wed, 15 Apr 2020 23:16:44: 4000000 INFO @ Wed, 15 Apr 2020 23:16:49: 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, 15 Apr 2020 23:16:53: 6000000 INFO @ Wed, 15 Apr 2020 23:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:16:54: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:16:54: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:16:55: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:16:55: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:16:55: #1 total tags in treatment: 6269239 INFO @ Wed, 15 Apr 2020 23:16:55: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:16:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:16:55: #1 tags after filtering in treatment: 6269239 INFO @ Wed, 15 Apr 2020 23:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:16:55: #1 finished! INFO @ Wed, 15 Apr 2020 23:16:55: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:16:55: #2 number of paired peaks: 783 WARNING @ Wed, 15 Apr 2020 23:16:55: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Wed, 15 Apr 2020 23:16:55: start model_add_line... INFO @ Wed, 15 Apr 2020 23:16:55: start X-correlation... INFO @ Wed, 15 Apr 2020 23:16:55: end of X-cor INFO @ Wed, 15 Apr 2020 23:16:55: #2 finished! INFO @ Wed, 15 Apr 2020 23:16:55: #2 predicted fragment length is 112 bps INFO @ Wed, 15 Apr 2020 23:16:55: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 15 Apr 2020 23:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.05_model.r INFO @ Wed, 15 Apr 2020 23:16:55: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:17:00: 1000000 INFO @ Wed, 15 Apr 2020 23:17:06: 2000000 INFO @ Wed, 15 Apr 2020 23:17:08: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:17:11: 3000000 INFO @ Wed, 15 Apr 2020 23:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.05_summits.bed INFO @ Wed, 15 Apr 2020 23:17:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4145 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:17:16: 4000000 INFO @ Wed, 15 Apr 2020 23:17:21: 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 @ Wed, 15 Apr 2020 23:17:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 15 Apr 2020 23:17:24: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:17:24: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:17:27: 6000000 INFO @ Wed, 15 Apr 2020 23:17:28: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:17:28: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:17:28: #1 total tags in treatment: 6269239 INFO @ Wed, 15 Apr 2020 23:17:28: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:17:28: #1 tags after filtering in treatment: 6269239 INFO @ Wed, 15 Apr 2020 23:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:17:28: #1 finished! INFO @ Wed, 15 Apr 2020 23:17:28: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:17:28: #2 number of paired peaks: 783 WARNING @ Wed, 15 Apr 2020 23:17:28: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Wed, 15 Apr 2020 23:17:28: start model_add_line... INFO @ Wed, 15 Apr 2020 23:17:29: start X-correlation... INFO @ Wed, 15 Apr 2020 23:17:29: end of X-cor INFO @ Wed, 15 Apr 2020 23:17:29: #2 finished! INFO @ Wed, 15 Apr 2020 23:17:29: #2 predicted fragment length is 112 bps INFO @ Wed, 15 Apr 2020 23:17:29: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 15 Apr 2020 23:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.10_model.r INFO @ Wed, 15 Apr 2020 23:17:29: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:17:30: 1000000 INFO @ Wed, 15 Apr 2020 23:17:35: 2000000 INFO @ Wed, 15 Apr 2020 23:17:40: 3000000 INFO @ Wed, 15 Apr 2020 23:17:42: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:17:45: 4000000 INFO @ Wed, 15 Apr 2020 23:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.10_summits.bed INFO @ Wed, 15 Apr 2020 23:17:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2314 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:17:50: 5000000 INFO @ Wed, 15 Apr 2020 23:17:55: 6000000 INFO @ Wed, 15 Apr 2020 23:17:56: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:17:56: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:17:56: #1 total tags in treatment: 6269239 INFO @ Wed, 15 Apr 2020 23:17:56: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:17:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:17:56: #1 tags after filtering in treatment: 6269239 INFO @ Wed, 15 Apr 2020 23:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:17:56: #1 finished! INFO @ Wed, 15 Apr 2020 23:17:56: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:17:57: #2 number of paired peaks: 783 WARNING @ Wed, 15 Apr 2020 23:17:57: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Wed, 15 Apr 2020 23:17:57: start model_add_line... INFO @ Wed, 15 Apr 2020 23:17:57: start X-correlation... INFO @ Wed, 15 Apr 2020 23:17:57: end of X-cor INFO @ Wed, 15 Apr 2020 23:17:57: #2 finished! INFO @ Wed, 15 Apr 2020 23:17:57: #2 predicted fragment length is 112 bps INFO @ Wed, 15 Apr 2020 23:17:57: #2 alternative fragment length(s) may be 112 bps INFO @ Wed, 15 Apr 2020 23:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.20_model.r INFO @ Wed, 15 Apr 2020 23:17:57: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:18:10: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7635313/SRX7635313.20_summits.bed INFO @ Wed, 15 Apr 2020 23:18:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1085 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。