Job ID = 5720157 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T12:15:42 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 ) 2020-04-15T12:15:42 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 : 20,623,272 reads read : 41,246,544 reads written : 20,623,272 reads 0-length : 20,623,272 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: 00:04:21 20623272 reads; of these: 20623272 (100.00%) were unpaired; of these: 206918 (1.00%) aligned 0 times 17014320 (82.50%) aligned exactly 1 time 3402034 (16.50%) aligned >1 times 99.00% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 4298549 / 20416354 = 0.2105 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 21:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.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 21:27:22: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:27:22: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:27:27: 1000000 INFO @ Wed, 15 Apr 2020 21:27:32: 2000000 INFO @ Wed, 15 Apr 2020 21:27:37: 3000000 INFO @ Wed, 15 Apr 2020 21:27:43: 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 21:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.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 21:27:48: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:27:48: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:27:49: 5000000 INFO @ Wed, 15 Apr 2020 21:27:53: 1000000 INFO @ Wed, 15 Apr 2020 21:27:54: 6000000 INFO @ Wed, 15 Apr 2020 21:27:59: 2000000 INFO @ Wed, 15 Apr 2020 21:28:00: 7000000 INFO @ Wed, 15 Apr 2020 21:28:04: 3000000 INFO @ Wed, 15 Apr 2020 21:28:05: 8000000 INFO @ Wed, 15 Apr 2020 21:28:09: 4000000 INFO @ Wed, 15 Apr 2020 21:28:10: 9000000 INFO @ Wed, 15 Apr 2020 21:28:14: 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 21:28:16: 10000000 INFO @ Wed, 15 Apr 2020 21:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.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 21:28:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:28:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:28:19: 6000000 INFO @ Wed, 15 Apr 2020 21:28:21: 11000000 INFO @ Wed, 15 Apr 2020 21:28:24: 1000000 INFO @ Wed, 15 Apr 2020 21:28:25: 7000000 INFO @ Wed, 15 Apr 2020 21:28:27: 12000000 INFO @ Wed, 15 Apr 2020 21:28:30: 2000000 INFO @ Wed, 15 Apr 2020 21:28:31: 8000000 INFO @ Wed, 15 Apr 2020 21:28:32: 13000000 INFO @ Wed, 15 Apr 2020 21:28:37: 3000000 INFO @ Wed, 15 Apr 2020 21:28:37: 14000000 INFO @ Wed, 15 Apr 2020 21:28:38: 9000000 INFO @ Wed, 15 Apr 2020 21:28:43: 15000000 INFO @ Wed, 15 Apr 2020 21:28:43: 4000000 INFO @ Wed, 15 Apr 2020 21:28:44: 10000000 INFO @ Wed, 15 Apr 2020 21:28:49: 16000000 INFO @ Wed, 15 Apr 2020 21:28:49: 5000000 INFO @ Wed, 15 Apr 2020 21:28:49: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:28:49: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:28:49: #1 total tags in treatment: 16117805 INFO @ Wed, 15 Apr 2020 21:28:49: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:28:49: #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 21:28:50: #1 tags after filtering in treatment: 16117805 INFO @ Wed, 15 Apr 2020 21:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:28:50: #1 finished! INFO @ Wed, 15 Apr 2020 21:28:50: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:28:50: 11000000 INFO @ Wed, 15 Apr 2020 21:28:51: #2 number of paired peaks: 173 WARNING @ Wed, 15 Apr 2020 21:28:51: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Wed, 15 Apr 2020 21:28:51: start model_add_line... INFO @ Wed, 15 Apr 2020 21:28:51: start X-correlation... INFO @ Wed, 15 Apr 2020 21:28:51: end of X-cor INFO @ Wed, 15 Apr 2020 21:28:51: #2 finished! INFO @ Wed, 15 Apr 2020 21:28:51: #2 predicted fragment length is 48 bps INFO @ Wed, 15 Apr 2020 21:28:51: #2 alternative fragment length(s) may be 2,48,203,443,469,590 bps INFO @ Wed, 15 Apr 2020 21:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.05_model.r WARNING @ Wed, 15 Apr 2020 21:28:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:28:51: #2 You may need to consider one of the other alternative d(s): 2,48,203,443,469,590 WARNING @ Wed, 15 Apr 2020 21:28:51: #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 21:28:51: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:28:55: 6000000 INFO @ Wed, 15 Apr 2020 21:28:55: 12000000 INFO @ Wed, 15 Apr 2020 21:29:01: 7000000 INFO @ Wed, 15 Apr 2020 21:29:01: 13000000 INFO @ Wed, 15 Apr 2020 21:29:06: 8000000 INFO @ Wed, 15 Apr 2020 21:29:07: 14000000 INFO @ Wed, 15 Apr 2020 21:29:13: 9000000 INFO @ Wed, 15 Apr 2020 21:29:13: 15000000 INFO @ Wed, 15 Apr 2020 21:29:16: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 21:29:18: 10000000 INFO @ Wed, 15 Apr 2020 21:29:18: 16000000 INFO @ Wed, 15 Apr 2020 21:29:19: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:29:19: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:29:19: #1 total tags in treatment: 16117805 INFO @ Wed, 15 Apr 2020 21:29:19: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:29:19: #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 21:29:19: #1 tags after filtering in treatment: 16117805 INFO @ Wed, 15 Apr 2020 21:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:29:20: #1 finished! INFO @ Wed, 15 Apr 2020 21:29:20: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:29:21: #2 number of paired peaks: 173 WARNING @ Wed, 15 Apr 2020 21:29:21: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Wed, 15 Apr 2020 21:29:21: start model_add_line... INFO @ Wed, 15 Apr 2020 21:29:21: start X-correlation... INFO @ Wed, 15 Apr 2020 21:29:21: end of X-cor INFO @ Wed, 15 Apr 2020 21:29:21: #2 finished! INFO @ Wed, 15 Apr 2020 21:29:21: #2 predicted fragment length is 48 bps INFO @ Wed, 15 Apr 2020 21:29:21: #2 alternative fragment length(s) may be 2,48,203,443,469,590 bps INFO @ Wed, 15 Apr 2020 21:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.10_model.r WARNING @ Wed, 15 Apr 2020 21:29:21: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:29:21: #2 You may need to consider one of the other alternative d(s): 2,48,203,443,469,590 WARNING @ Wed, 15 Apr 2020 21:29:21: #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 21:29:21: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:29:24: 11000000 INFO @ Wed, 15 Apr 2020 21:29:29: 12000000 INFO @ Wed, 15 Apr 2020 21:29:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.05_peaks.xls INFO @ Wed, 15 Apr 2020 21:29:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 21:29:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.05_summits.bed INFO @ Wed, 15 Apr 2020 21:29:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 21:29:34: 13000000 INFO @ Wed, 15 Apr 2020 21:29:40: 14000000 INFO @ Wed, 15 Apr 2020 21:29:45: 15000000 INFO @ Wed, 15 Apr 2020 21:29:46: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 21:29:50: 16000000 INFO @ Wed, 15 Apr 2020 21:29:51: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:29:51: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:29:51: #1 total tags in treatment: 16117805 INFO @ Wed, 15 Apr 2020 21:29:51: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:29:51: #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 21:29:51: #1 tags after filtering in treatment: 16117805 INFO @ Wed, 15 Apr 2020 21:29:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:29:51: #1 finished! INFO @ Wed, 15 Apr 2020 21:29:51: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:29:52: #2 number of paired peaks: 173 WARNING @ Wed, 15 Apr 2020 21:29:52: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Wed, 15 Apr 2020 21:29:52: start model_add_line... INFO @ Wed, 15 Apr 2020 21:29:52: start X-correlation... INFO @ Wed, 15 Apr 2020 21:29:53: end of X-cor INFO @ Wed, 15 Apr 2020 21:29:53: #2 finished! INFO @ Wed, 15 Apr 2020 21:29:53: #2 predicted fragment length is 48 bps INFO @ Wed, 15 Apr 2020 21:29:53: #2 alternative fragment length(s) may be 2,48,203,443,469,590 bps INFO @ Wed, 15 Apr 2020 21:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.20_model.r WARNING @ Wed, 15 Apr 2020 21:29:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:29:53: #2 You may need to consider one of the other alternative d(s): 2,48,203,443,469,590 WARNING @ Wed, 15 Apr 2020 21:29:53: #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 21:29:53: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:29:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.10_peaks.xls INFO @ Wed, 15 Apr 2020 21:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 21:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.10_summits.bed INFO @ Wed, 15 Apr 2020 21:30:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 21:30:18: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 21:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.20_peaks.xls INFO @ Wed, 15 Apr 2020 21:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 21:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5702599/SRX5702599.20_summits.bed INFO @ Wed, 15 Apr 2020 21:30:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (86 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。