Job ID = 2590173 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:53:12 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 ) 2019-08-12T10:53:27 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 ) 2019-08-12T10:53:27 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 : 16,047,878 reads read : 16,047,878 reads written : 16,047,878 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: 00:03:33 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1452009 (9.05%) aligned 0 times 12365378 (77.05%) aligned exactly 1 time 2230491 (13.90%) aligned >1 times 90.95% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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_rmdupse_core] 1646486 / 14595869 = 0.1128 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 12 Aug 2019 20:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.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 @ Mon, 12 Aug 2019 20:11:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.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 @ Mon, 12 Aug 2019 20:11:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.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 @ Mon, 12 Aug 2019 20:11:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:11:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:11:35: 1000000 INFO @ Mon, 12 Aug 2019 20:11:36: 1000000 INFO @ Mon, 12 Aug 2019 20:11:37: 1000000 INFO @ Mon, 12 Aug 2019 20:11:43: 2000000 INFO @ Mon, 12 Aug 2019 20:11:44: 2000000 INFO @ Mon, 12 Aug 2019 20:11:45: 2000000 INFO @ Mon, 12 Aug 2019 20:11:50: 3000000 INFO @ Mon, 12 Aug 2019 20:11:51: 3000000 INFO @ Mon, 12 Aug 2019 20:11:52: 3000000 INFO @ Mon, 12 Aug 2019 20:11:58: 4000000 INFO @ Mon, 12 Aug 2019 20:11:59: 4000000 INFO @ Mon, 12 Aug 2019 20:12:00: 4000000 INFO @ Mon, 12 Aug 2019 20:12:06: 5000000 INFO @ Mon, 12 Aug 2019 20:12:06: 5000000 INFO @ Mon, 12 Aug 2019 20:12:07: 5000000 INFO @ Mon, 12 Aug 2019 20:12:13: 6000000 INFO @ Mon, 12 Aug 2019 20:12:14: 6000000 INFO @ Mon, 12 Aug 2019 20:12:15: 6000000 INFO @ Mon, 12 Aug 2019 20:12:21: 7000000 INFO @ Mon, 12 Aug 2019 20:12:22: 7000000 INFO @ Mon, 12 Aug 2019 20:12:22: 7000000 INFO @ Mon, 12 Aug 2019 20:12:28: 8000000 INFO @ Mon, 12 Aug 2019 20:12:29: 8000000 INFO @ Mon, 12 Aug 2019 20:12:30: 8000000 INFO @ Mon, 12 Aug 2019 20:12:36: 9000000 INFO @ Mon, 12 Aug 2019 20:12:37: 9000000 INFO @ Mon, 12 Aug 2019 20:12:37: 9000000 INFO @ Mon, 12 Aug 2019 20:12:44: 10000000 INFO @ Mon, 12 Aug 2019 20:12:44: 10000000 INFO @ Mon, 12 Aug 2019 20:12:45: 10000000 INFO @ Mon, 12 Aug 2019 20:12:51: 11000000 INFO @ Mon, 12 Aug 2019 20:12:52: 11000000 INFO @ Mon, 12 Aug 2019 20:12:53: 11000000 INFO @ Mon, 12 Aug 2019 20:12:59: 12000000 INFO @ Mon, 12 Aug 2019 20:12:59: 12000000 INFO @ Mon, 12 Aug 2019 20:13:00: 12000000 INFO @ Mon, 12 Aug 2019 20:13:06: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:13:06: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:13:06: #1 total tags in treatment: 12949383 INFO @ Mon, 12 Aug 2019 20:13:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:13:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:13:06: #1 tags after filtering in treatment: 12949383 INFO @ Mon, 12 Aug 2019 20:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:13:06: #1 finished! INFO @ Mon, 12 Aug 2019 20:13:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:13:07: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:13:07: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:13:07: #1 total tags in treatment: 12949383 INFO @ Mon, 12 Aug 2019 20:13:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:13:07: #1 tags after filtering in treatment: 12949383 INFO @ Mon, 12 Aug 2019 20:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:13:07: #1 finished! INFO @ Mon, 12 Aug 2019 20:13:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:13:07: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:13:07: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:13:07: #1 total tags in treatment: 12949383 INFO @ Mon, 12 Aug 2019 20:13:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:13:07: #2 number of paired peaks: 268 WARNING @ Mon, 12 Aug 2019 20:13:07: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 12 Aug 2019 20:13:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:13:07: start X-correlation... INFO @ Mon, 12 Aug 2019 20:13:07: #1 tags after filtering in treatment: 12949383 INFO @ Mon, 12 Aug 2019 20:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:13:07: #1 finished! INFO @ Mon, 12 Aug 2019 20:13:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:13:07: end of X-cor INFO @ Mon, 12 Aug 2019 20:13:07: #2 finished! INFO @ Mon, 12 Aug 2019 20:13:07: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 20:13:07: #2 alternative fragment length(s) may be 1,41,578 bps INFO @ Mon, 12 Aug 2019 20:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.05_model.r WARNING @ Mon, 12 Aug 2019 20:13:07: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:13:07: #2 You may need to consider one of the other alternative d(s): 1,41,578 WARNING @ Mon, 12 Aug 2019 20:13:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:13:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:13:08: #2 number of paired peaks: 268 WARNING @ Mon, 12 Aug 2019 20:13:08: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 12 Aug 2019 20:13:08: start model_add_line... INFO @ Mon, 12 Aug 2019 20:13:08: start X-correlation... INFO @ Mon, 12 Aug 2019 20:13:08: end of X-cor INFO @ Mon, 12 Aug 2019 20:13:08: #2 finished! INFO @ Mon, 12 Aug 2019 20:13:08: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 20:13:08: #2 alternative fragment length(s) may be 1,41,578 bps INFO @ Mon, 12 Aug 2019 20:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.10_model.r WARNING @ Mon, 12 Aug 2019 20:13:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:13:08: #2 You may need to consider one of the other alternative d(s): 1,41,578 WARNING @ Mon, 12 Aug 2019 20:13:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:13:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:13:09: #2 number of paired peaks: 268 WARNING @ Mon, 12 Aug 2019 20:13:09: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 12 Aug 2019 20:13:09: start model_add_line... INFO @ Mon, 12 Aug 2019 20:13:09: start X-correlation... INFO @ Mon, 12 Aug 2019 20:13:09: end of X-cor INFO @ Mon, 12 Aug 2019 20:13:09: #2 finished! INFO @ Mon, 12 Aug 2019 20:13:09: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 20:13:09: #2 alternative fragment length(s) may be 1,41,578 bps INFO @ Mon, 12 Aug 2019 20:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.20_model.r WARNING @ Mon, 12 Aug 2019 20:13:09: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:13:09: #2 You may need to consider one of the other alternative d(s): 1,41,578 WARNING @ Mon, 12 Aug 2019 20:13:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:13:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:13:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.10_summits.bed INFO @ Mon, 12 Aug 2019 20:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:56: Done! INFO @ Mon, 12 Aug 2019 20:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.05_summits.bed INFO @ Mon, 12 Aug 2019 20:13:56: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (353 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (630 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495061/SRX495061.20_summits.bed INFO @ Mon, 12 Aug 2019 20:13:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (115 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。