Job ID = 5720233 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T13:36:31 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 : 29,509,495 reads read : 29,509,495 reads written : 29,509,495 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: 00:06:22 29509495 reads; of these: 29509495 (100.00%) were unpaired; of these: 1396861 (4.73%) aligned 0 times 23386183 (79.25%) aligned exactly 1 time 4726451 (16.02%) aligned >1 times 95.27% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 11913383 / 28112634 = 0.4238 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 22:50:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.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 22:50:16: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:50:16: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:50:21: 1000000 INFO @ Wed, 15 Apr 2020 22:50:26: 2000000 INFO @ Wed, 15 Apr 2020 22:50:31: 3000000 INFO @ Wed, 15 Apr 2020 22:50:35: 4000000 INFO @ Wed, 15 Apr 2020 22:50:40: 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 22:50:45: 6000000 INFO @ Wed, 15 Apr 2020 22:50:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.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 22:50:46: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:50:46: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:50:50: 7000000 INFO @ Wed, 15 Apr 2020 22:50:51: 1000000 INFO @ Wed, 15 Apr 2020 22:50:55: 8000000 INFO @ Wed, 15 Apr 2020 22:50:56: 2000000 INFO @ Wed, 15 Apr 2020 22:51:00: 9000000 INFO @ Wed, 15 Apr 2020 22:51:01: 3000000 INFO @ Wed, 15 Apr 2020 22:51:05: 10000000 INFO @ Wed, 15 Apr 2020 22:51:06: 4000000 INFO @ Wed, 15 Apr 2020 22:51:10: 11000000 INFO @ Wed, 15 Apr 2020 22:51:11: 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 22:51:15: 12000000 INFO @ Wed, 15 Apr 2020 22:51:16: 6000000 INFO @ Wed, 15 Apr 2020 22:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.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 22:51:16: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:51:16: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:51:20: 13000000 INFO @ Wed, 15 Apr 2020 22:51:21: 7000000 INFO @ Wed, 15 Apr 2020 22:51:21: 1000000 INFO @ Wed, 15 Apr 2020 22:51:25: 14000000 INFO @ Wed, 15 Apr 2020 22:51:26: 8000000 INFO @ Wed, 15 Apr 2020 22:51:26: 2000000 INFO @ Wed, 15 Apr 2020 22:51:31: 15000000 INFO @ Wed, 15 Apr 2020 22:51:31: 9000000 INFO @ Wed, 15 Apr 2020 22:51:31: 3000000 INFO @ Wed, 15 Apr 2020 22:51:36: 16000000 INFO @ Wed, 15 Apr 2020 22:51:36: 10000000 INFO @ Wed, 15 Apr 2020 22:51:36: 4000000 INFO @ Wed, 15 Apr 2020 22:51:37: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:51:37: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:51:37: #1 total tags in treatment: 16199251 INFO @ Wed, 15 Apr 2020 22:51:37: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:51:37: #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 22:51:37: #1 tags after filtering in treatment: 16199251 INFO @ Wed, 15 Apr 2020 22:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:51:37: #1 finished! INFO @ Wed, 15 Apr 2020 22:51:37: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:51:38: #2 number of paired peaks: 385 WARNING @ Wed, 15 Apr 2020 22:51:38: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Wed, 15 Apr 2020 22:51:38: start model_add_line... INFO @ Wed, 15 Apr 2020 22:51:38: start X-correlation... INFO @ Wed, 15 Apr 2020 22:51:38: end of X-cor INFO @ Wed, 15 Apr 2020 22:51:38: #2 finished! INFO @ Wed, 15 Apr 2020 22:51:38: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:51:38: #2 alternative fragment length(s) may be 1,32,580,595 bps INFO @ Wed, 15 Apr 2020 22:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.05_model.r WARNING @ Wed, 15 Apr 2020 22:51:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:51:38: #2 You may need to consider one of the other alternative d(s): 1,32,580,595 WARNING @ Wed, 15 Apr 2020 22:51:38: #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 22:51:38: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:51:41: 11000000 INFO @ Wed, 15 Apr 2020 22:51:42: 5000000 INFO @ Wed, 15 Apr 2020 22:51:46: 12000000 INFO @ Wed, 15 Apr 2020 22:51:46: 6000000 INFO @ Wed, 15 Apr 2020 22:51:51: 13000000 INFO @ Wed, 15 Apr 2020 22:51:52: 7000000 INFO @ Wed, 15 Apr 2020 22:51:56: 14000000 INFO @ Wed, 15 Apr 2020 22:51:57: 8000000 INFO @ Wed, 15 Apr 2020 22:52:01: 15000000 INFO @ Wed, 15 Apr 2020 22:52:02: 9000000 INFO @ Wed, 15 Apr 2020 22:52:05: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:52:06: 16000000 INFO @ Wed, 15 Apr 2020 22:52:07: 10000000 INFO @ Wed, 15 Apr 2020 22:52:08: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:52:08: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:52:08: #1 total tags in treatment: 16199251 INFO @ Wed, 15 Apr 2020 22:52:08: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:52:08: #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 22:52:08: #1 tags after filtering in treatment: 16199251 INFO @ Wed, 15 Apr 2020 22:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:52:08: #1 finished! INFO @ Wed, 15 Apr 2020 22:52:08: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:52:09: #2 number of paired peaks: 385 WARNING @ Wed, 15 Apr 2020 22:52:09: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Wed, 15 Apr 2020 22:52:09: start model_add_line... INFO @ Wed, 15 Apr 2020 22:52:09: start X-correlation... INFO @ Wed, 15 Apr 2020 22:52:09: end of X-cor INFO @ Wed, 15 Apr 2020 22:52:09: #2 finished! INFO @ Wed, 15 Apr 2020 22:52:09: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:52:09: #2 alternative fragment length(s) may be 1,32,580,595 bps INFO @ Wed, 15 Apr 2020 22:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.10_model.r WARNING @ Wed, 15 Apr 2020 22:52:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:52:09: #2 You may need to consider one of the other alternative d(s): 1,32,580,595 WARNING @ Wed, 15 Apr 2020 22:52:09: #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 22:52:09: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:52:12: 11000000 INFO @ Wed, 15 Apr 2020 22:52:17: 12000000 INFO @ Wed, 15 Apr 2020 22:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.05_summits.bed INFO @ Wed, 15 Apr 2020 22:52:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:52:21: 13000000 INFO @ Wed, 15 Apr 2020 22:52:26: 14000000 INFO @ Wed, 15 Apr 2020 22:52:31: 15000000 INFO @ Wed, 15 Apr 2020 22:52:35: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:52:36: 16000000 INFO @ Wed, 15 Apr 2020 22:52:37: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:52:37: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:52:37: #1 total tags in treatment: 16199251 INFO @ Wed, 15 Apr 2020 22:52:37: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:52:37: #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 22:52:37: #1 tags after filtering in treatment: 16199251 INFO @ Wed, 15 Apr 2020 22:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:52:37: #1 finished! INFO @ Wed, 15 Apr 2020 22:52:37: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:52:38: #2 number of paired peaks: 385 WARNING @ Wed, 15 Apr 2020 22:52:38: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Wed, 15 Apr 2020 22:52:38: start model_add_line... INFO @ Wed, 15 Apr 2020 22:52:38: start X-correlation... INFO @ Wed, 15 Apr 2020 22:52:38: end of X-cor INFO @ Wed, 15 Apr 2020 22:52:38: #2 finished! INFO @ Wed, 15 Apr 2020 22:52:38: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 22:52:38: #2 alternative fragment length(s) may be 1,32,580,595 bps INFO @ Wed, 15 Apr 2020 22:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.20_model.r WARNING @ Wed, 15 Apr 2020 22:52:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:52:38: #2 You may need to consider one of the other alternative d(s): 1,32,580,595 WARNING @ Wed, 15 Apr 2020 22:52:38: #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 22:52:38: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.10_summits.bed INFO @ Wed, 15 Apr 2020 22:52:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:53:05: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:53:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:53:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720163/SRX6720163.20_summits.bed INFO @ Wed, 15 Apr 2020 22:53:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。