Job ID = 5720310 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:06:13 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 ) 2020-04-15T14:06:13 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 : 13,642,872 reads read : 13,642,872 reads written : 13,642,872 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: 00:02:09 13642872 reads; of these: 13642872 (100.00%) were unpaired; of these: 5412106 (39.67%) aligned 0 times 6872229 (50.37%) aligned exactly 1 time 1358537 (9.96%) aligned >1 times 60.33% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 1387309 / 8230766 = 0.1686 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 23:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.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 23:13:54: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:13:54: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:14:00: 1000000 INFO @ Wed, 15 Apr 2020 23:14:06: 2000000 INFO @ Wed, 15 Apr 2020 23:14:12: 3000000 INFO @ Wed, 15 Apr 2020 23:14:18: 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, 15 Apr 2020 23:14:24: 5000000 INFO @ Wed, 15 Apr 2020 23:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.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 23:14:24: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:14:24: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:14:31: 6000000 INFO @ Wed, 15 Apr 2020 23:14:31: 1000000 INFO @ Wed, 15 Apr 2020 23:14:36: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:14:36: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:14:36: #1 total tags in treatment: 6843457 INFO @ Wed, 15 Apr 2020 23:14:36: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:14:36: #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 23:14:36: #1 tags after filtering in treatment: 6843457 INFO @ Wed, 15 Apr 2020 23:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:14:36: #1 finished! INFO @ Wed, 15 Apr 2020 23:14:36: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:14:37: #2 number of paired peaks: 365 WARNING @ Wed, 15 Apr 2020 23:14:37: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Wed, 15 Apr 2020 23:14:37: start model_add_line... INFO @ Wed, 15 Apr 2020 23:14:37: start X-correlation... INFO @ Wed, 15 Apr 2020 23:14:37: end of X-cor INFO @ Wed, 15 Apr 2020 23:14:37: #2 finished! INFO @ Wed, 15 Apr 2020 23:14:37: #2 predicted fragment length is 59 bps INFO @ Wed, 15 Apr 2020 23:14:37: #2 alternative fragment length(s) may be 59 bps INFO @ Wed, 15 Apr 2020 23:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.05_model.r WARNING @ Wed, 15 Apr 2020 23:14:37: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:14:37: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Wed, 15 Apr 2020 23:14:37: #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 23:14:37: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:14:38: 2000000 INFO @ Wed, 15 Apr 2020 23:14:44: 3000000 INFO @ Wed, 15 Apr 2020 23:14:51: 4000000 INFO @ Wed, 15 Apr 2020 23:14:51: #3 Call peaks for each chromosome... 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 23:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.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 23:14:54: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:14:54: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:14:57: 5000000 INFO @ Wed, 15 Apr 2020 23:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.05_summits.bed INFO @ Wed, 15 Apr 2020 23:14:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (703 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:15:01: 1000000 INFO @ Wed, 15 Apr 2020 23:15:04: 6000000 INFO @ Wed, 15 Apr 2020 23:15:08: 2000000 INFO @ Wed, 15 Apr 2020 23:15:09: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:15:09: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:15:09: #1 total tags in treatment: 6843457 INFO @ Wed, 15 Apr 2020 23:15:09: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:15:09: #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 23:15:10: #1 tags after filtering in treatment: 6843457 INFO @ Wed, 15 Apr 2020 23:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:15:10: #1 finished! INFO @ Wed, 15 Apr 2020 23:15:10: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:15:10: #2 number of paired peaks: 365 WARNING @ Wed, 15 Apr 2020 23:15:10: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Wed, 15 Apr 2020 23:15:10: start model_add_line... INFO @ Wed, 15 Apr 2020 23:15:10: start X-correlation... INFO @ Wed, 15 Apr 2020 23:15:10: end of X-cor INFO @ Wed, 15 Apr 2020 23:15:10: #2 finished! INFO @ Wed, 15 Apr 2020 23:15:10: #2 predicted fragment length is 59 bps INFO @ Wed, 15 Apr 2020 23:15:10: #2 alternative fragment length(s) may be 59 bps INFO @ Wed, 15 Apr 2020 23:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.10_model.r WARNING @ Wed, 15 Apr 2020 23:15:10: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:15:10: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Wed, 15 Apr 2020 23:15:10: #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 23:15:10: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:15:15: 3000000 INFO @ Wed, 15 Apr 2020 23:15:21: 4000000 INFO @ Wed, 15 Apr 2020 23:15:24: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:15:27: 5000000 INFO @ Wed, 15 Apr 2020 23:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.10_summits.bed INFO @ Wed, 15 Apr 2020 23:15:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:15:33: 6000000 INFO @ Wed, 15 Apr 2020 23:15:38: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:15:38: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:15:38: #1 total tags in treatment: 6843457 INFO @ Wed, 15 Apr 2020 23:15:38: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:15:38: #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 23:15:38: #1 tags after filtering in treatment: 6843457 INFO @ Wed, 15 Apr 2020 23:15:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:15:38: #1 finished! INFO @ Wed, 15 Apr 2020 23:15:38: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:15:39: #2 number of paired peaks: 365 WARNING @ Wed, 15 Apr 2020 23:15:39: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Wed, 15 Apr 2020 23:15:39: start model_add_line... INFO @ Wed, 15 Apr 2020 23:15:39: start X-correlation... INFO @ Wed, 15 Apr 2020 23:15:39: end of X-cor INFO @ Wed, 15 Apr 2020 23:15:39: #2 finished! INFO @ Wed, 15 Apr 2020 23:15:39: #2 predicted fragment length is 59 bps INFO @ Wed, 15 Apr 2020 23:15:39: #2 alternative fragment length(s) may be 59 bps INFO @ Wed, 15 Apr 2020 23:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.20_model.r WARNING @ Wed, 15 Apr 2020 23:15:39: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:15:39: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Wed, 15 Apr 2020 23:15:39: #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 23:15:39: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:15:53: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627595/SRX7627595.20_summits.bed INFO @ Wed, 15 Apr 2020 23:16:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。