Job ID = 2589970 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:52:07 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 : 15,082,416 reads read : 15,082,416 reads written : 15,082,416 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163567.sra.cache’: 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: 00:02:45 15082416 reads; of these: 15082416 (100.00%) were unpaired; of these: 734915 (4.87%) aligned 0 times 12498442 (82.87%) aligned exactly 1 time 1849059 (12.26%) aligned >1 times 95.13% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 4299664 / 14347501 = 0.2997 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 19:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.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 19:00:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.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 19:00:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.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 19:00:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:49: 1000000 INFO @ Mon, 12 Aug 2019 19:00:50: 1000000 INFO @ Mon, 12 Aug 2019 19:00:52: 1000000 INFO @ Mon, 12 Aug 2019 19:00:56: 2000000 INFO @ Mon, 12 Aug 2019 19:00:57: 2000000 INFO @ Mon, 12 Aug 2019 19:00:59: 2000000 INFO @ Mon, 12 Aug 2019 19:01:02: 3000000 INFO @ Mon, 12 Aug 2019 19:01:03: 3000000 INFO @ Mon, 12 Aug 2019 19:01:05: 3000000 INFO @ Mon, 12 Aug 2019 19:01:08: 4000000 INFO @ Mon, 12 Aug 2019 19:01:09: 4000000 INFO @ Mon, 12 Aug 2019 19:01:12: 4000000 INFO @ Mon, 12 Aug 2019 19:01:15: 5000000 INFO @ Mon, 12 Aug 2019 19:01:15: 5000000 INFO @ Mon, 12 Aug 2019 19:01:19: 5000000 INFO @ Mon, 12 Aug 2019 19:01:21: 6000000 INFO @ Mon, 12 Aug 2019 19:01:22: 6000000 INFO @ Mon, 12 Aug 2019 19:01:26: 6000000 INFO @ Mon, 12 Aug 2019 19:01:27: 7000000 INFO @ Mon, 12 Aug 2019 19:01:28: 7000000 INFO @ Mon, 12 Aug 2019 19:01:32: 7000000 INFO @ Mon, 12 Aug 2019 19:01:34: 8000000 INFO @ Mon, 12 Aug 2019 19:01:34: 8000000 INFO @ Mon, 12 Aug 2019 19:01:39: 8000000 INFO @ Mon, 12 Aug 2019 19:01:40: 9000000 INFO @ Mon, 12 Aug 2019 19:01:41: 9000000 INFO @ Mon, 12 Aug 2019 19:01:46: 9000000 INFO @ Mon, 12 Aug 2019 19:01:46: 10000000 INFO @ Mon, 12 Aug 2019 19:01:47: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:01:47: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:01:47: #1 total tags in treatment: 10047837 INFO @ Mon, 12 Aug 2019 19:01:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:47: #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 19:01:47: #1 tags after filtering in treatment: 10047837 INFO @ Mon, 12 Aug 2019 19:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:47: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:47: 10000000 INFO @ Mon, 12 Aug 2019 19:01:47: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:01:47: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:01:47: #1 total tags in treatment: 10047837 INFO @ Mon, 12 Aug 2019 19:01:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:47: #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 19:01:48: #1 tags after filtering in treatment: 10047837 INFO @ Mon, 12 Aug 2019 19:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:48: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:48: #2 number of paired peaks: 336 WARNING @ Mon, 12 Aug 2019 19:01:48: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:48: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:48: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:48: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:48: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:48: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:01:48: #2 alternative fragment length(s) may be 3,41,581,584 bps INFO @ Mon, 12 Aug 2019 19:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.05_model.r WARNING @ Mon, 12 Aug 2019 19:01:48: #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 19:01:48: #2 You may need to consider one of the other alternative d(s): 3,41,581,584 WARNING @ Mon, 12 Aug 2019 19:01:48: #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 19:01:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:49: #2 number of paired peaks: 336 WARNING @ Mon, 12 Aug 2019 19:01:49: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:49: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:49: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:49: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:49: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:49: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:01:49: #2 alternative fragment length(s) may be 3,41,581,584 bps INFO @ Mon, 12 Aug 2019 19:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.10_model.r WARNING @ Mon, 12 Aug 2019 19:01:49: #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 19:01:49: #2 You may need to consider one of the other alternative d(s): 3,41,581,584 WARNING @ Mon, 12 Aug 2019 19:01:49: #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 19:01:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:53: 10000000 INFO @ Mon, 12 Aug 2019 19:01:53: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:01:53: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:01:53: #1 total tags in treatment: 10047837 INFO @ Mon, 12 Aug 2019 19:01:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:53: #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 19:01:53: #1 tags after filtering in treatment: 10047837 INFO @ Mon, 12 Aug 2019 19:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:53: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:54: #2 number of paired peaks: 336 WARNING @ Mon, 12 Aug 2019 19:01:54: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:54: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:54: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:54: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:54: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:54: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:01:54: #2 alternative fragment length(s) may be 3,41,581,584 bps INFO @ Mon, 12 Aug 2019 19:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.20_model.r WARNING @ Mon, 12 Aug 2019 19:01:54: #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 19:01:54: #2 You may need to consider one of the other alternative d(s): 3,41,581,584 WARNING @ Mon, 12 Aug 2019 19:01:54: #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 19:01:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.05_summits.bed INFO @ Mon, 12 Aug 2019 19:02:28: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1412 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.10_summits.bed INFO @ Mon, 12 Aug 2019 19:02:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (332 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466501/SRX466501.20_summits.bed INFO @ Mon, 12 Aug 2019 19:02:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (89 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。