Job ID = 5720324 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:30:31 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 : 21,768,229 reads read : 21,768,229 reads written : 21,768,229 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: 00:07:17 21768229 reads; of these: 21768229 (100.00%) were unpaired; of these: 805761 (3.70%) aligned 0 times 16115177 (74.03%) aligned exactly 1 time 4847291 (22.27%) aligned >1 times 96.30% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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 12 files... [bam_rmdupse_core] 3817453 / 20962468 = 0.1821 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 23:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.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 23:49:50: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:49:50: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:49:56: 1000000 INFO @ Wed, 15 Apr 2020 23:50:02: 2000000 INFO @ Wed, 15 Apr 2020 23:50:07: 3000000 INFO @ Wed, 15 Apr 2020 23:50:13: 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 23:50:19: 5000000 INFO @ Wed, 15 Apr 2020 23:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.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 23:50:20: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:50:20: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:50:25: 6000000 INFO @ Wed, 15 Apr 2020 23:50:26: 1000000 INFO @ Wed, 15 Apr 2020 23:50:31: 7000000 INFO @ Wed, 15 Apr 2020 23:50:32: 2000000 INFO @ Wed, 15 Apr 2020 23:50:37: 8000000 INFO @ Wed, 15 Apr 2020 23:50:38: 3000000 INFO @ Wed, 15 Apr 2020 23:50:43: 9000000 INFO @ Wed, 15 Apr 2020 23:50:44: 4000000 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 23:50:50: 10000000 INFO @ Wed, 15 Apr 2020 23:50:50: 5000000 INFO @ Wed, 15 Apr 2020 23:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.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 23:50:50: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:50:50: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:50:56: 11000000 INFO @ Wed, 15 Apr 2020 23:50:57: 6000000 INFO @ Wed, 15 Apr 2020 23:50:59: 1000000 INFO @ Wed, 15 Apr 2020 23:51:02: 12000000 INFO @ Wed, 15 Apr 2020 23:51:03: 7000000 INFO @ Wed, 15 Apr 2020 23:51:07: 2000000 INFO @ Wed, 15 Apr 2020 23:51:08: 13000000 INFO @ Wed, 15 Apr 2020 23:51:09: 8000000 INFO @ Wed, 15 Apr 2020 23:51:14: 14000000 INFO @ Wed, 15 Apr 2020 23:51:15: 3000000 INFO @ Wed, 15 Apr 2020 23:51:16: 9000000 INFO @ Wed, 15 Apr 2020 23:51:21: 15000000 INFO @ Wed, 15 Apr 2020 23:51:22: 10000000 INFO @ Wed, 15 Apr 2020 23:51:24: 4000000 INFO @ Wed, 15 Apr 2020 23:51:27: 16000000 INFO @ Wed, 15 Apr 2020 23:51:29: 11000000 INFO @ Wed, 15 Apr 2020 23:51:33: 5000000 INFO @ Wed, 15 Apr 2020 23:51:33: 17000000 INFO @ Wed, 15 Apr 2020 23:51:34: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:51:34: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:51:34: #1 total tags in treatment: 17145015 INFO @ Wed, 15 Apr 2020 23:51:34: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:51:34: #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 23:51:35: 12000000 INFO @ Wed, 15 Apr 2020 23:51:35: #1 tags after filtering in treatment: 17145015 INFO @ Wed, 15 Apr 2020 23:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:51:35: #1 finished! INFO @ Wed, 15 Apr 2020 23:51:35: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:51:36: #2 number of paired peaks: 367 WARNING @ Wed, 15 Apr 2020 23:51:36: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Wed, 15 Apr 2020 23:51:36: start model_add_line... INFO @ Wed, 15 Apr 2020 23:51:36: start X-correlation... INFO @ Wed, 15 Apr 2020 23:51:36: end of X-cor INFO @ Wed, 15 Apr 2020 23:51:36: #2 finished! INFO @ Wed, 15 Apr 2020 23:51:36: #2 predicted fragment length is 63 bps INFO @ Wed, 15 Apr 2020 23:51:36: #2 alternative fragment length(s) may be 2,50,56,63 bps INFO @ Wed, 15 Apr 2020 23:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.05_model.r WARNING @ Wed, 15 Apr 2020 23:51:36: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:51:36: #2 You may need to consider one of the other alternative d(s): 2,50,56,63 WARNING @ Wed, 15 Apr 2020 23:51:36: #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 23:51:36: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:51:40: 13000000 INFO @ Wed, 15 Apr 2020 23:51:41: 6000000 INFO @ Wed, 15 Apr 2020 23:51:46: 14000000 INFO @ Wed, 15 Apr 2020 23:51:49: 7000000 INFO @ Wed, 15 Apr 2020 23:51:52: 15000000 INFO @ Wed, 15 Apr 2020 23:51:57: 8000000 INFO @ Wed, 15 Apr 2020 23:51:59: 16000000 INFO @ Wed, 15 Apr 2020 23:52:05: 17000000 INFO @ Wed, 15 Apr 2020 23:52:06: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:52:06: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:52:06: #1 total tags in treatment: 17145015 INFO @ Wed, 15 Apr 2020 23:52:06: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:52:06: #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 23:52:06: 9000000 INFO @ Wed, 15 Apr 2020 23:52:06: #1 tags after filtering in treatment: 17145015 INFO @ Wed, 15 Apr 2020 23:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:52:06: #1 finished! INFO @ Wed, 15 Apr 2020 23:52:06: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:52:07: #2 number of paired peaks: 367 WARNING @ Wed, 15 Apr 2020 23:52:07: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Wed, 15 Apr 2020 23:52:07: start model_add_line... INFO @ Wed, 15 Apr 2020 23:52:07: start X-correlation... INFO @ Wed, 15 Apr 2020 23:52:07: end of X-cor INFO @ Wed, 15 Apr 2020 23:52:07: #2 finished! INFO @ Wed, 15 Apr 2020 23:52:07: #2 predicted fragment length is 63 bps INFO @ Wed, 15 Apr 2020 23:52:07: #2 alternative fragment length(s) may be 2,50,56,63 bps INFO @ Wed, 15 Apr 2020 23:52:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.10_model.r WARNING @ Wed, 15 Apr 2020 23:52:07: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:52:07: #2 You may need to consider one of the other alternative d(s): 2,50,56,63 WARNING @ Wed, 15 Apr 2020 23:52:07: #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 23:52:07: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:52:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:52:08: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:52:14: 10000000 INFO @ Wed, 15 Apr 2020 23:52:20: 11000000 INFO @ Wed, 15 Apr 2020 23:52:28: 12000000 INFO @ Wed, 15 Apr 2020 23:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.05_summits.bed INFO @ Wed, 15 Apr 2020 23:52:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1706 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:52:36: 13000000 INFO @ Wed, 15 Apr 2020 23:52:42: 14000000 INFO @ Wed, 15 Apr 2020 23:52:46: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:52:48: 15000000 INFO @ Wed, 15 Apr 2020 23:52:55: 16000000 INFO @ Wed, 15 Apr 2020 23:53:02: 17000000 INFO @ Wed, 15 Apr 2020 23:53:04: #1 tag size is determined as 76 bps INFO @ Wed, 15 Apr 2020 23:53:04: #1 tag size = 76 INFO @ Wed, 15 Apr 2020 23:53:04: #1 total tags in treatment: 17145015 INFO @ Wed, 15 Apr 2020 23:53:04: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:53:04: #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 23:53:04: #1 tags after filtering in treatment: 17145015 INFO @ Wed, 15 Apr 2020 23:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:53:04: #1 finished! INFO @ Wed, 15 Apr 2020 23:53:04: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.10_summits.bed INFO @ Wed, 15 Apr 2020 23:53:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:53:05: #2 number of paired peaks: 367 WARNING @ Wed, 15 Apr 2020 23:53:05: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Wed, 15 Apr 2020 23:53:05: start model_add_line... INFO @ Wed, 15 Apr 2020 23:53:05: start X-correlation... INFO @ Wed, 15 Apr 2020 23:53:05: end of X-cor INFO @ Wed, 15 Apr 2020 23:53:05: #2 finished! INFO @ Wed, 15 Apr 2020 23:53:05: #2 predicted fragment length is 63 bps INFO @ Wed, 15 Apr 2020 23:53:05: #2 alternative fragment length(s) may be 2,50,56,63 bps INFO @ Wed, 15 Apr 2020 23:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.20_model.r WARNING @ Wed, 15 Apr 2020 23:53:05: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:53:05: #2 You may need to consider one of the other alternative d(s): 2,50,56,63 WARNING @ Wed, 15 Apr 2020 23:53:05: #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 23:53:05: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:53:40: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971794/SRX7971794.20_summits.bed INFO @ Wed, 15 Apr 2020 23:53:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (266 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。