Job ID = 5720312 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:05:09 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 ) 2020-04-15T14:08:46 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 ) 2020-04-15T14:09:08 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 : 13,561,672 reads read : 13,561,672 reads written : 13,561,672 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: 00:03:12 13561672 reads; of these: 13561672 (100.00%) were unpaired; of these: 659095 (4.86%) aligned 0 times 10787927 (79.55%) aligned exactly 1 time 2114650 (15.59%) aligned >1 times 95.14% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3542285 / 12902577 = 0.2745 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 23:17:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.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 23:17:02: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:17:02: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:17:09: 1000000 INFO @ Wed, 15 Apr 2020 23:17:15: 2000000 INFO @ Wed, 15 Apr 2020 23:17:21: 3000000 INFO @ Wed, 15 Apr 2020 23:17:26: 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 23:17:31: 5000000 INFO @ Wed, 15 Apr 2020 23:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.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 23:17:32: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:17:32: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:17:37: 6000000 INFO @ Wed, 15 Apr 2020 23:17:38: 1000000 INFO @ Wed, 15 Apr 2020 23:17:43: 7000000 INFO @ Wed, 15 Apr 2020 23:17:44: 2000000 INFO @ Wed, 15 Apr 2020 23:17:49: 8000000 INFO @ Wed, 15 Apr 2020 23:17:49: 3000000 INFO @ Wed, 15 Apr 2020 23:17:54: 9000000 INFO @ Wed, 15 Apr 2020 23:17:55: 4000000 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: 9360292 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 23:17:57: #1 tags after filtering in treatment: 9360292 INFO @ Wed, 15 Apr 2020 23:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:17:57: #1 finished! INFO @ Wed, 15 Apr 2020 23:17:57: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:17:57: #2 number of paired peaks: 406 WARNING @ Wed, 15 Apr 2020 23:17:57: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 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 49 bps INFO @ Wed, 15 Apr 2020 23:17:57: #2 alternative fragment length(s) may be 3,49,576 bps INFO @ Wed, 15 Apr 2020 23:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.05_model.r WARNING @ Wed, 15 Apr 2020 23:17:57: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:17:57: #2 You may need to consider one of the other alternative d(s): 3,49,576 WARNING @ Wed, 15 Apr 2020 23:17:57: #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 23:17:57: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:17:57: #3 Pre-compute pvalue-qvalue table... 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 23:18:01: 5000000 INFO @ Wed, 15 Apr 2020 23:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.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 23:18:02: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:18:02: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:18:06: 6000000 INFO @ Wed, 15 Apr 2020 23:18:08: 1000000 INFO @ Wed, 15 Apr 2020 23:18:12: 7000000 INFO @ Wed, 15 Apr 2020 23:18:14: 2000000 INFO @ Wed, 15 Apr 2020 23:18:16: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:18:18: 8000000 INFO @ Wed, 15 Apr 2020 23:18:19: 3000000 INFO @ Wed, 15 Apr 2020 23:18:24: 9000000 INFO @ Wed, 15 Apr 2020 23:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.05_summits.bed INFO @ Wed, 15 Apr 2020 23:18:25: Done! INFO @ Wed, 15 Apr 2020 23:18:25: 4000000 INFO @ Wed, 15 Apr 2020 23:18:26: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:18:26: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:18:26: #1 total tags in treatment: 9360292 INFO @ Wed, 15 Apr 2020 23:18:26: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:18:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (716 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:18:26: #1 tags after filtering in treatment: 9360292 INFO @ Wed, 15 Apr 2020 23:18:26: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:18:26: #1 finished! INFO @ Wed, 15 Apr 2020 23:18:26: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:18:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:18:26: #2 number of paired peaks: 406 WARNING @ Wed, 15 Apr 2020 23:18:26: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Wed, 15 Apr 2020 23:18:26: start model_add_line... INFO @ Wed, 15 Apr 2020 23:18:27: start X-correlation... INFO @ Wed, 15 Apr 2020 23:18:27: end of X-cor INFO @ Wed, 15 Apr 2020 23:18:27: #2 finished! INFO @ Wed, 15 Apr 2020 23:18:27: #2 predicted fragment length is 49 bps INFO @ Wed, 15 Apr 2020 23:18:27: #2 alternative fragment length(s) may be 3,49,576 bps INFO @ Wed, 15 Apr 2020 23:18:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.10_model.r WARNING @ Wed, 15 Apr 2020 23:18:27: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:18:27: #2 You may need to consider one of the other alternative d(s): 3,49,576 WARNING @ Wed, 15 Apr 2020 23:18:27: #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 23:18:27: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:18:31: 5000000 INFO @ Wed, 15 Apr 2020 23:18:36: 6000000 INFO @ Wed, 15 Apr 2020 23:18:42: 7000000 INFO @ Wed, 15 Apr 2020 23:18:45: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:18:47: 8000000 INFO @ Wed, 15 Apr 2020 23:18:53: 9000000 INFO @ Wed, 15 Apr 2020 23:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.10_summits.bed INFO @ Wed, 15 Apr 2020 23:18:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (472 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:18:55: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:18:55: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:18:55: #1 total tags in treatment: 9360292 INFO @ Wed, 15 Apr 2020 23:18:55: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:18:55: #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 23:18:55: #1 tags after filtering in treatment: 9360292 INFO @ Wed, 15 Apr 2020 23:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:18:55: #1 finished! INFO @ Wed, 15 Apr 2020 23:18:55: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:18:55: #2 number of paired peaks: 406 WARNING @ Wed, 15 Apr 2020 23:18:55: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Wed, 15 Apr 2020 23:18:55: start model_add_line... INFO @ Wed, 15 Apr 2020 23:18:56: start X-correlation... INFO @ Wed, 15 Apr 2020 23:18:56: end of X-cor INFO @ Wed, 15 Apr 2020 23:18:56: #2 finished! INFO @ Wed, 15 Apr 2020 23:18:56: #2 predicted fragment length is 49 bps INFO @ Wed, 15 Apr 2020 23:18:56: #2 alternative fragment length(s) may be 3,49,576 bps INFO @ Wed, 15 Apr 2020 23:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.20_model.r WARNING @ Wed, 15 Apr 2020 23:18:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:18:56: #2 You may need to consider one of the other alternative d(s): 3,49,576 WARNING @ Wed, 15 Apr 2020 23:18:56: #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 23:18:56: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:19:14: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:19:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:19:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:19:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7627596/SRX7627596.20_summits.bed INFO @ Wed, 15 Apr 2020 23:19:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (202 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。