Job ID = 2589357 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T08:45:33 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 : 30,520,033 reads read : 30,520,033 reads written : 30,520,033 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: 00:07:24 30520033 reads; of these: 30520033 (100.00%) were unpaired; of these: 1808938 (5.93%) aligned 0 times 24179728 (79.23%) aligned exactly 1 time 4531367 (14.85%) aligned >1 times 94.07% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 4299734 / 28711095 = 0.1498 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 18:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.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 18:02:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:02:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:02:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.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 18:02:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:02:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.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 18:02:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:02:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:02:44: 1000000 INFO @ Mon, 12 Aug 2019 18:02:44: 1000000 INFO @ Mon, 12 Aug 2019 18:02:47: 1000000 INFO @ Mon, 12 Aug 2019 18:02:52: 2000000 INFO @ Mon, 12 Aug 2019 18:02:52: 2000000 INFO @ Mon, 12 Aug 2019 18:02:56: 2000000 INFO @ Mon, 12 Aug 2019 18:03:00: 3000000 INFO @ Mon, 12 Aug 2019 18:03:00: 3000000 INFO @ Mon, 12 Aug 2019 18:03:05: 3000000 INFO @ Mon, 12 Aug 2019 18:03:08: 4000000 INFO @ Mon, 12 Aug 2019 18:03:08: 4000000 INFO @ Mon, 12 Aug 2019 18:03:14: 4000000 INFO @ Mon, 12 Aug 2019 18:03:16: 5000000 INFO @ Mon, 12 Aug 2019 18:03:16: 5000000 INFO @ Mon, 12 Aug 2019 18:03:23: 5000000 INFO @ Mon, 12 Aug 2019 18:03:24: 6000000 INFO @ Mon, 12 Aug 2019 18:03:24: 6000000 INFO @ Mon, 12 Aug 2019 18:03:31: 7000000 INFO @ Mon, 12 Aug 2019 18:03:32: 6000000 INFO @ Mon, 12 Aug 2019 18:03:32: 7000000 INFO @ Mon, 12 Aug 2019 18:03:39: 8000000 INFO @ Mon, 12 Aug 2019 18:03:39: 8000000 INFO @ Mon, 12 Aug 2019 18:03:41: 7000000 INFO @ Mon, 12 Aug 2019 18:03:47: 9000000 INFO @ Mon, 12 Aug 2019 18:03:47: 9000000 INFO @ Mon, 12 Aug 2019 18:03:49: 8000000 INFO @ Mon, 12 Aug 2019 18:03:55: 10000000 INFO @ Mon, 12 Aug 2019 18:03:55: 10000000 INFO @ Mon, 12 Aug 2019 18:03:58: 9000000 INFO @ Mon, 12 Aug 2019 18:04:03: 11000000 INFO @ Mon, 12 Aug 2019 18:04:03: 11000000 INFO @ Mon, 12 Aug 2019 18:04:07: 10000000 INFO @ Mon, 12 Aug 2019 18:04:11: 12000000 INFO @ Mon, 12 Aug 2019 18:04:11: 12000000 INFO @ Mon, 12 Aug 2019 18:04:16: 11000000 INFO @ Mon, 12 Aug 2019 18:04:19: 13000000 INFO @ Mon, 12 Aug 2019 18:04:19: 13000000 INFO @ Mon, 12 Aug 2019 18:04:25: 12000000 INFO @ Mon, 12 Aug 2019 18:04:26: 14000000 INFO @ Mon, 12 Aug 2019 18:04:27: 14000000 INFO @ Mon, 12 Aug 2019 18:04:33: 13000000 INFO @ Mon, 12 Aug 2019 18:04:34: 15000000 INFO @ Mon, 12 Aug 2019 18:04:34: 15000000 INFO @ Mon, 12 Aug 2019 18:04:42: 14000000 INFO @ Mon, 12 Aug 2019 18:04:42: 16000000 INFO @ Mon, 12 Aug 2019 18:04:42: 16000000 INFO @ Mon, 12 Aug 2019 18:04:50: 17000000 INFO @ Mon, 12 Aug 2019 18:04:50: 17000000 INFO @ Mon, 12 Aug 2019 18:04:50: 15000000 INFO @ Mon, 12 Aug 2019 18:04:58: 18000000 INFO @ Mon, 12 Aug 2019 18:04:58: 18000000 INFO @ Mon, 12 Aug 2019 18:04:59: 16000000 INFO @ Mon, 12 Aug 2019 18:05:06: 19000000 INFO @ Mon, 12 Aug 2019 18:05:06: 19000000 INFO @ Mon, 12 Aug 2019 18:05:08: 17000000 INFO @ Mon, 12 Aug 2019 18:05:13: 20000000 INFO @ Mon, 12 Aug 2019 18:05:14: 20000000 INFO @ Mon, 12 Aug 2019 18:05:17: 18000000 INFO @ Mon, 12 Aug 2019 18:05:21: 21000000 INFO @ Mon, 12 Aug 2019 18:05:21: 21000000 INFO @ Mon, 12 Aug 2019 18:05:26: 19000000 INFO @ Mon, 12 Aug 2019 18:05:29: 22000000 INFO @ Mon, 12 Aug 2019 18:05:29: 22000000 INFO @ Mon, 12 Aug 2019 18:05:35: 20000000 INFO @ Mon, 12 Aug 2019 18:05:37: 23000000 INFO @ Mon, 12 Aug 2019 18:05:37: 23000000 INFO @ Mon, 12 Aug 2019 18:05:43: 21000000 INFO @ Mon, 12 Aug 2019 18:05:45: 24000000 INFO @ Mon, 12 Aug 2019 18:05:45: 24000000 INFO @ Mon, 12 Aug 2019 18:05:48: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:05:48: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:05:48: #1 total tags in treatment: 24411361 INFO @ Mon, 12 Aug 2019 18:05:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:05:48: #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 18:05:48: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:05:48: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:05:48: #1 total tags in treatment: 24411361 INFO @ Mon, 12 Aug 2019 18:05:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:05:48: #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 18:05:49: #1 tags after filtering in treatment: 24411361 INFO @ Mon, 12 Aug 2019 18:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:05:49: #1 finished! INFO @ Mon, 12 Aug 2019 18:05:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:05:49: #1 tags after filtering in treatment: 24411361 INFO @ Mon, 12 Aug 2019 18:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:05:49: #1 finished! INFO @ Mon, 12 Aug 2019 18:05:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:05:51: #2 number of paired peaks: 139 WARNING @ Mon, 12 Aug 2019 18:05:51: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 12 Aug 2019 18:05:51: start model_add_line... INFO @ Mon, 12 Aug 2019 18:05:51: #2 number of paired peaks: 139 WARNING @ Mon, 12 Aug 2019 18:05:51: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 12 Aug 2019 18:05:51: start model_add_line... INFO @ Mon, 12 Aug 2019 18:05:51: start X-correlation... INFO @ Mon, 12 Aug 2019 18:05:51: end of X-cor INFO @ Mon, 12 Aug 2019 18:05:51: #2 finished! INFO @ Mon, 12 Aug 2019 18:05:51: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:05:51: #2 alternative fragment length(s) may be 1,45,106,110,445,479,513,555 bps INFO @ Mon, 12 Aug 2019 18:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.05_model.r WARNING @ Mon, 12 Aug 2019 18:05:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:05:51: #2 You may need to consider one of the other alternative d(s): 1,45,106,110,445,479,513,555 WARNING @ Mon, 12 Aug 2019 18:05:51: #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 18:05:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:05:51: start X-correlation... INFO @ Mon, 12 Aug 2019 18:05:51: end of X-cor INFO @ Mon, 12 Aug 2019 18:05:51: #2 finished! INFO @ Mon, 12 Aug 2019 18:05:51: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:05:51: #2 alternative fragment length(s) may be 1,45,106,110,445,479,513,555 bps INFO @ Mon, 12 Aug 2019 18:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.10_model.r WARNING @ Mon, 12 Aug 2019 18:05:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:05:51: #2 You may need to consider one of the other alternative d(s): 1,45,106,110,445,479,513,555 WARNING @ Mon, 12 Aug 2019 18:05:51: #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 18:05:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:05:52: 22000000 INFO @ Mon, 12 Aug 2019 18:06:00: 23000000 INFO @ Mon, 12 Aug 2019 18:06:09: 24000000 INFO @ Mon, 12 Aug 2019 18:06:12: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:06:12: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:06:12: #1 total tags in treatment: 24411361 INFO @ Mon, 12 Aug 2019 18:06:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:06:12: #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 18:06:13: #1 tags after filtering in treatment: 24411361 INFO @ Mon, 12 Aug 2019 18:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:06:13: #1 finished! INFO @ Mon, 12 Aug 2019 18:06:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:06:15: #2 number of paired peaks: 139 WARNING @ Mon, 12 Aug 2019 18:06:15: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Mon, 12 Aug 2019 18:06:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:06:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:06:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:06:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:06:15: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:06:15: #2 alternative fragment length(s) may be 1,45,106,110,445,479,513,555 bps INFO @ Mon, 12 Aug 2019 18:06:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.20_model.r WARNING @ Mon, 12 Aug 2019 18:06:15: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:06:15: #2 You may need to consider one of the other alternative d(s): 1,45,106,110,445,479,513,555 WARNING @ Mon, 12 Aug 2019 18:06:15: #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 18:06:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:06:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:06:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:06:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.10_summits.bed INFO @ Mon, 12 Aug 2019 18:07:03: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.05_summits.bed INFO @ Mon, 12 Aug 2019 18:07:03: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:07:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:07:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:07:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078710/SRX1078710.20_summits.bed INFO @ Mon, 12 Aug 2019 18:07:27: 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。