Job ID = 5720304 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T13:59:46 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 ) 2020-04-15T13:59:46 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 ) 2020-04-15T13:59:46 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 : 5,781,099 reads read : 5,781,099 reads written : 5,781,099 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:10 5781099 reads; of these: 5781099 (100.00%) were unpaired; of these: 516786 (8.94%) aligned 0 times 4355196 (75.34%) aligned exactly 1 time 909117 (15.73%) aligned >1 times 91.06% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 4910479 / 5264313 = 0.9328 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 23:02:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.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 23:02:39: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:02:39: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:02:41: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:02:41: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:02:41: #1 total tags in treatment: 353834 INFO @ Wed, 15 Apr 2020 23:02:41: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:02:41: #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 23:02:41: #1 tags after filtering in treatment: 353834 INFO @ Wed, 15 Apr 2020 23:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:02:41: #1 finished! INFO @ Wed, 15 Apr 2020 23:02:41: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:02:41: #2 number of paired peaks: 1203 INFO @ Wed, 15 Apr 2020 23:02:41: start model_add_line... INFO @ Wed, 15 Apr 2020 23:02:41: start X-correlation... INFO @ Wed, 15 Apr 2020 23:02:41: end of X-cor INFO @ Wed, 15 Apr 2020 23:02:41: #2 finished! INFO @ Wed, 15 Apr 2020 23:02:41: #2 predicted fragment length is 55 bps INFO @ Wed, 15 Apr 2020 23:02:41: #2 alternative fragment length(s) may be 55,151,476,518 bps INFO @ Wed, 15 Apr 2020 23:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.05_model.r WARNING @ Wed, 15 Apr 2020 23:02:41: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:02:41: #2 You may need to consider one of the other alternative d(s): 55,151,476,518 WARNING @ Wed, 15 Apr 2020 23:02:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:02:41: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:02:42: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.05_summits.bed INFO @ Wed, 15 Apr 2020 23:02:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (342 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 23:03:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.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 23:03:07: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:03:07: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:03:09: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:03:09: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:03:09: #1 total tags in treatment: 353834 INFO @ Wed, 15 Apr 2020 23:03:09: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:03:09: #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 23:03:09: #1 tags after filtering in treatment: 353834 INFO @ Wed, 15 Apr 2020 23:03:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:03:09: #1 finished! INFO @ Wed, 15 Apr 2020 23:03:09: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:03:09: #2 number of paired peaks: 1203 INFO @ Wed, 15 Apr 2020 23:03:09: start model_add_line... INFO @ Wed, 15 Apr 2020 23:03:09: start X-correlation... INFO @ Wed, 15 Apr 2020 23:03:09: end of X-cor INFO @ Wed, 15 Apr 2020 23:03:09: #2 finished! INFO @ Wed, 15 Apr 2020 23:03:09: #2 predicted fragment length is 55 bps INFO @ Wed, 15 Apr 2020 23:03:09: #2 alternative fragment length(s) may be 55,151,476,518 bps INFO @ Wed, 15 Apr 2020 23:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.10_model.r WARNING @ Wed, 15 Apr 2020 23:03:09: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:03:09: #2 You may need to consider one of the other alternative d(s): 55,151,476,518 WARNING @ Wed, 15 Apr 2020 23:03:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:03:09: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:03:10: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.10_summits.bed INFO @ Wed, 15 Apr 2020 23:03:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 23:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.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 23:03:37: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:03:37: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 15 Apr 2020 23:03:39: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:03:39: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:03:39: #1 total tags in treatment: 353834 INFO @ Wed, 15 Apr 2020 23:03:39: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:03:39: #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 23:03:39: #1 tags after filtering in treatment: 353834 INFO @ Wed, 15 Apr 2020 23:03:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:03:39: #1 finished! INFO @ Wed, 15 Apr 2020 23:03:39: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:03:39: #2 number of paired peaks: 1203 INFO @ Wed, 15 Apr 2020 23:03:39: start model_add_line... INFO @ Wed, 15 Apr 2020 23:03:39: start X-correlation... INFO @ Wed, 15 Apr 2020 23:03:39: end of X-cor INFO @ Wed, 15 Apr 2020 23:03:39: #2 finished! INFO @ Wed, 15 Apr 2020 23:03:39: #2 predicted fragment length is 55 bps INFO @ Wed, 15 Apr 2020 23:03:39: #2 alternative fragment length(s) may be 55,151,476,518 bps INFO @ Wed, 15 Apr 2020 23:03:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.20_model.r WARNING @ Wed, 15 Apr 2020 23:03:39: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:03:39: #2 You may need to consider one of the other alternative d(s): 55,151,476,518 WARNING @ Wed, 15 Apr 2020 23:03:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:03:39: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:03:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:03:40: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627552/SRX7627552.20_summits.bed INFO @ Wed, 15 Apr 2020 23:03:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling