Job ID = 5720301 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T13:53:54 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 ) 2020-04-15T13:57:20 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 : 20,213,801 reads read : 40,427,602 reads written : 20,213,801 reads 0-length : 20,213,801 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: 00:04:54 20213801 reads; of these: 20213801 (100.00%) were unpaired; of these: 378443 (1.87%) aligned 0 times 16671623 (82.48%) aligned exactly 1 time 3163735 (15.65%) aligned >1 times 98.13% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 9317052 / 19835358 = 0.4697 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 23:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.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 23:08:08: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:08:08: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:08:13: 1000000 INFO @ Wed, 15 Apr 2020 23:08:18: 2000000 INFO @ Wed, 15 Apr 2020 23:08:23: 3000000 INFO @ Wed, 15 Apr 2020 23:08:28: 4000000 INFO @ Wed, 15 Apr 2020 23:08:33: 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 23:08:38: 6000000 INFO @ Wed, 15 Apr 2020 23:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.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 23:08:38: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:08:38: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:08:43: 7000000 INFO @ Wed, 15 Apr 2020 23:08:43: 1000000 INFO @ Wed, 15 Apr 2020 23:08:47: 8000000 INFO @ Wed, 15 Apr 2020 23:08:48: 2000000 INFO @ Wed, 15 Apr 2020 23:08:52: 9000000 INFO @ Wed, 15 Apr 2020 23:08:53: 3000000 INFO @ Wed, 15 Apr 2020 23:08:57: 10000000 INFO @ Wed, 15 Apr 2020 23:08:58: 4000000 INFO @ Wed, 15 Apr 2020 23:09:00: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:09:00: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:09:00: #1 total tags in treatment: 10518306 INFO @ Wed, 15 Apr 2020 23:09:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:09:00: #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 23:09:00: #1 tags after filtering in treatment: 10518306 INFO @ Wed, 15 Apr 2020 23:09:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:09:00: #1 finished! INFO @ Wed, 15 Apr 2020 23:09:00: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:09:01: #2 number of paired peaks: 397 WARNING @ Wed, 15 Apr 2020 23:09:01: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Wed, 15 Apr 2020 23:09:01: start model_add_line... INFO @ Wed, 15 Apr 2020 23:09:01: start X-correlation... INFO @ Wed, 15 Apr 2020 23:09:01: end of X-cor INFO @ Wed, 15 Apr 2020 23:09:01: #2 finished! INFO @ Wed, 15 Apr 2020 23:09:01: #2 predicted fragment length is 46 bps INFO @ Wed, 15 Apr 2020 23:09:01: #2 alternative fragment length(s) may be 2,46,536,576 bps INFO @ Wed, 15 Apr 2020 23:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.05_model.r WARNING @ Wed, 15 Apr 2020 23:09:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:09:01: #2 You may need to consider one of the other alternative d(s): 2,46,536,576 WARNING @ Wed, 15 Apr 2020 23:09:01: #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 23:09:01: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:09:03: 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 23:09:08: 6000000 INFO @ Wed, 15 Apr 2020 23:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.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 23:09:08: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:09:08: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:09:13: 7000000 INFO @ Wed, 15 Apr 2020 23:09:13: 1000000 INFO @ Wed, 15 Apr 2020 23:09:17: 8000000 INFO @ Wed, 15 Apr 2020 23:09:18: 2000000 INFO @ Wed, 15 Apr 2020 23:09:21: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:09:22: 9000000 INFO @ Wed, 15 Apr 2020 23:09:23: 3000000 INFO @ Wed, 15 Apr 2020 23:09:27: 10000000 INFO @ Wed, 15 Apr 2020 23:09:28: 4000000 INFO @ Wed, 15 Apr 2020 23:09:30: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:09:30: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:09:30: #1 total tags in treatment: 10518306 INFO @ Wed, 15 Apr 2020 23:09:30: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:09:30: #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 23:09:30: #1 tags after filtering in treatment: 10518306 INFO @ Wed, 15 Apr 2020 23:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:09:30: #1 finished! INFO @ Wed, 15 Apr 2020 23:09:30: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.05_summits.bed INFO @ Wed, 15 Apr 2020 23:09:30: Done! INFO @ Wed, 15 Apr 2020 23:09:30: #2 number of paired peaks: 397 WARNING @ Wed, 15 Apr 2020 23:09:30: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Wed, 15 Apr 2020 23:09:30: start model_add_line... INFO @ Wed, 15 Apr 2020 23:09:31: start X-correlation... INFO @ Wed, 15 Apr 2020 23:09:31: end of X-cor INFO @ Wed, 15 Apr 2020 23:09:31: #2 finished! INFO @ Wed, 15 Apr 2020 23:09:31: #2 predicted fragment length is 46 bps INFO @ Wed, 15 Apr 2020 23:09:31: #2 alternative fragment length(s) may be 2,46,536,576 bps INFO @ Wed, 15 Apr 2020 23:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.10_model.r WARNING @ Wed, 15 Apr 2020 23:09:31: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:09:31: #2 You may need to consider one of the other alternative d(s): 2,46,536,576 WARNING @ Wed, 15 Apr 2020 23:09:31: #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 23:09:31: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:09:31: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:09:33: 5000000 INFO @ Wed, 15 Apr 2020 23:09:38: 6000000 INFO @ Wed, 15 Apr 2020 23:09:42: 7000000 INFO @ Wed, 15 Apr 2020 23:09:47: 8000000 INFO @ Wed, 15 Apr 2020 23:09:51: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:09:52: 9000000 INFO @ Wed, 15 Apr 2020 23:09:57: 10000000 INFO @ Wed, 15 Apr 2020 23:10:00: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 23:10:00: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 23:10:00: #1 total tags in treatment: 10518306 INFO @ Wed, 15 Apr 2020 23:10:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:10:00: #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 23:10:00: #1 tags after filtering in treatment: 10518306 INFO @ Wed, 15 Apr 2020 23:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 23:10:00: #1 finished! INFO @ Wed, 15 Apr 2020 23:10:00: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:10:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:10:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:10:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.10_summits.bed INFO @ Wed, 15 Apr 2020 23:10:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 1 millis INFO @ Wed, 15 Apr 2020 23:10:00: #2 number of paired peaks: 397 WARNING @ Wed, 15 Apr 2020 23:10:00: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Wed, 15 Apr 2020 23:10:00: start model_add_line... CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:10:01: start X-correlation... INFO @ Wed, 15 Apr 2020 23:10:01: end of X-cor INFO @ Wed, 15 Apr 2020 23:10:01: #2 finished! INFO @ Wed, 15 Apr 2020 23:10:01: #2 predicted fragment length is 46 bps INFO @ Wed, 15 Apr 2020 23:10:01: #2 alternative fragment length(s) may be 2,46,536,576 bps INFO @ Wed, 15 Apr 2020 23:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.20_model.r WARNING @ Wed, 15 Apr 2020 23:10:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:10:01: #2 You may need to consider one of the other alternative d(s): 2,46,536,576 WARNING @ Wed, 15 Apr 2020 23:10:01: #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 23:10:01: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:10:21: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7574653/SRX7574653.20_summits.bed INFO @ Wed, 15 Apr 2020 23:10:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (177 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。