Job ID = 1292374 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T09:20:37 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 : 29,694,149 reads read : 59,388,298 reads written : 59,388,298 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:45:24 29694149 reads; of these: 29694149 (100.00%) were paired; of these: 2004716 (6.75%) aligned concordantly 0 times 24806828 (83.54%) aligned concordantly exactly 1 time 2882605 (9.71%) aligned concordantly >1 times ---- 2004716 pairs aligned concordantly 0 times; of these: 557500 (27.81%) aligned discordantly 1 time ---- 1447216 pairs aligned 0 times concordantly or discordantly; of these: 2894432 mates make up the pairs; of these: 2094703 (72.37%) aligned 0 times 528927 (18.27%) aligned exactly 1 time 270802 (9.36%) aligned >1 times 96.47% overall alignment rate Time searching: 00:45:25 Overall time: 00:45:25 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 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 14889772 / 28194217 = 0.5281 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 @ Sun, 02 Jun 2019 19:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.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 @ Sun, 02 Jun 2019 19:41:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:41:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.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 @ Sun, 02 Jun 2019 19:41:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:41:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.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 @ Sun, 02 Jun 2019 19:41:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:41:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:41:53: 1000000 INFO @ Sun, 02 Jun 2019 19:41:53: 1000000 INFO @ Sun, 02 Jun 2019 19:41:54: 1000000 INFO @ Sun, 02 Jun 2019 19:42:00: 2000000 INFO @ Sun, 02 Jun 2019 19:42:02: 2000000 INFO @ Sun, 02 Jun 2019 19:42:03: 2000000 INFO @ Sun, 02 Jun 2019 19:42:07: 3000000 INFO @ Sun, 02 Jun 2019 19:42:10: 3000000 INFO @ Sun, 02 Jun 2019 19:42:13: 3000000 INFO @ Sun, 02 Jun 2019 19:42:15: 4000000 INFO @ Sun, 02 Jun 2019 19:42:18: 4000000 INFO @ Sun, 02 Jun 2019 19:42:22: 4000000 INFO @ Sun, 02 Jun 2019 19:42:23: 5000000 INFO @ Sun, 02 Jun 2019 19:42:27: 5000000 INFO @ Sun, 02 Jun 2019 19:42:30: 6000000 INFO @ Sun, 02 Jun 2019 19:42:32: 5000000 INFO @ Sun, 02 Jun 2019 19:42:35: 6000000 INFO @ Sun, 02 Jun 2019 19:42:38: 7000000 INFO @ Sun, 02 Jun 2019 19:42:41: 6000000 INFO @ Sun, 02 Jun 2019 19:42:43: 7000000 INFO @ Sun, 02 Jun 2019 19:42:45: 8000000 INFO @ Sun, 02 Jun 2019 19:42:50: 7000000 INFO @ Sun, 02 Jun 2019 19:42:51: 8000000 INFO @ Sun, 02 Jun 2019 19:42:53: 9000000 INFO @ Sun, 02 Jun 2019 19:42:59: 9000000 INFO @ Sun, 02 Jun 2019 19:43:00: 8000000 INFO @ Sun, 02 Jun 2019 19:43:00: 10000000 INFO @ Sun, 02 Jun 2019 19:43:07: 10000000 INFO @ Sun, 02 Jun 2019 19:43:07: 11000000 INFO @ Sun, 02 Jun 2019 19:43:09: 9000000 INFO @ Sun, 02 Jun 2019 19:43:15: 12000000 INFO @ Sun, 02 Jun 2019 19:43:16: 11000000 INFO @ Sun, 02 Jun 2019 19:43:18: 10000000 INFO @ Sun, 02 Jun 2019 19:43:22: 13000000 INFO @ Sun, 02 Jun 2019 19:43:24: 12000000 INFO @ Sun, 02 Jun 2019 19:43:27: 11000000 INFO @ Sun, 02 Jun 2019 19:43:29: 14000000 INFO @ Sun, 02 Jun 2019 19:43:32: 13000000 INFO @ Sun, 02 Jun 2019 19:43:36: 15000000 INFO @ Sun, 02 Jun 2019 19:43:37: 12000000 INFO @ Sun, 02 Jun 2019 19:43:40: 14000000 INFO @ Sun, 02 Jun 2019 19:43:44: 16000000 INFO @ Sun, 02 Jun 2019 19:43:46: 13000000 INFO @ Sun, 02 Jun 2019 19:43:49: 15000000 INFO @ Sun, 02 Jun 2019 19:43:51: 17000000 INFO @ Sun, 02 Jun 2019 19:43:55: 14000000 INFO @ Sun, 02 Jun 2019 19:43:57: 16000000 INFO @ Sun, 02 Jun 2019 19:43:58: 18000000 INFO @ Sun, 02 Jun 2019 19:44:05: 15000000 INFO @ Sun, 02 Jun 2019 19:44:05: 17000000 INFO @ Sun, 02 Jun 2019 19:44:05: 19000000 INFO @ Sun, 02 Jun 2019 19:44:12: 20000000 INFO @ Sun, 02 Jun 2019 19:44:13: 18000000 INFO @ Sun, 02 Jun 2019 19:44:14: 16000000 INFO @ Sun, 02 Jun 2019 19:44:19: 21000000 INFO @ Sun, 02 Jun 2019 19:44:21: 19000000 INFO @ Sun, 02 Jun 2019 19:44:24: 17000000 INFO @ Sun, 02 Jun 2019 19:44:26: 22000000 INFO @ Sun, 02 Jun 2019 19:44:29: 20000000 INFO @ Sun, 02 Jun 2019 19:44:33: 18000000 INFO @ Sun, 02 Jun 2019 19:44:34: 23000000 INFO @ Sun, 02 Jun 2019 19:44:37: 21000000 INFO @ Sun, 02 Jun 2019 19:44:41: 24000000 INFO @ Sun, 02 Jun 2019 19:44:41: 19000000 INFO @ Sun, 02 Jun 2019 19:44:44: 22000000 INFO @ Sun, 02 Jun 2019 19:44:48: 25000000 INFO @ Sun, 02 Jun 2019 19:44:50: 20000000 INFO @ Sun, 02 Jun 2019 19:44:52: 23000000 INFO @ Sun, 02 Jun 2019 19:44:55: 26000000 INFO @ Sun, 02 Jun 2019 19:44:59: 21000000 INFO @ Sun, 02 Jun 2019 19:45:00: 24000000 INFO @ Sun, 02 Jun 2019 19:45:02: 27000000 INFO @ Sun, 02 Jun 2019 19:45:06: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:45:06: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:45:06: #1 total tags in treatment: 12961623 INFO @ Sun, 02 Jun 2019 19:45:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:45:06: #1 tags after filtering in treatment: 11029079 INFO @ Sun, 02 Jun 2019 19:45:06: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 02 Jun 2019 19:45:06: #1 finished! INFO @ Sun, 02 Jun 2019 19:45:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:45:07: #2 number of paired peaks: 459 WARNING @ Sun, 02 Jun 2019 19:45:07: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 02 Jun 2019 19:45:07: start model_add_line... INFO @ Sun, 02 Jun 2019 19:45:07: start X-correlation... INFO @ Sun, 02 Jun 2019 19:45:07: end of X-cor INFO @ Sun, 02 Jun 2019 19:45:07: #2 finished! INFO @ Sun, 02 Jun 2019 19:45:07: #2 predicted fragment length is 127 bps INFO @ Sun, 02 Jun 2019 19:45:07: #2 alternative fragment length(s) may be 4,127,142 bps INFO @ Sun, 02 Jun 2019 19:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.10_model.r WARNING @ Sun, 02 Jun 2019 19:45:07: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:45:07: #2 You may need to consider one of the other alternative d(s): 4,127,142 WARNING @ Sun, 02 Jun 2019 19:45:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:45:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:45:08: 25000000 INFO @ Sun, 02 Jun 2019 19:45:08: 22000000 INFO @ Sun, 02 Jun 2019 19:45:16: 26000000 INFO @ Sun, 02 Jun 2019 19:45:17: 23000000 INFO @ Sun, 02 Jun 2019 19:45:24: 27000000 INFO @ Sun, 02 Jun 2019 19:45:25: 24000000 INFO @ Sun, 02 Jun 2019 19:45:28: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:45:28: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:45:28: #1 total tags in treatment: 12961623 INFO @ Sun, 02 Jun 2019 19:45:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:45:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:45:28: #1 tags after filtering in treatment: 11029079 INFO @ Sun, 02 Jun 2019 19:45:28: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 02 Jun 2019 19:45:28: #1 finished! INFO @ Sun, 02 Jun 2019 19:45:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:45:29: #2 number of paired peaks: 459 WARNING @ Sun, 02 Jun 2019 19:45:29: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 02 Jun 2019 19:45:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:45:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:45:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:45:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:45:29: #2 predicted fragment length is 127 bps INFO @ Sun, 02 Jun 2019 19:45:29: #2 alternative fragment length(s) may be 4,127,142 bps INFO @ Sun, 02 Jun 2019 19:45:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.20_model.r WARNING @ Sun, 02 Jun 2019 19:45:29: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:45:29: #2 You may need to consider one of the other alternative d(s): 4,127,142 WARNING @ Sun, 02 Jun 2019 19:45:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:45:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:45:34: 25000000 INFO @ Sun, 02 Jun 2019 19:45:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:45:43: 26000000 INFO @ Sun, 02 Jun 2019 19:45:52: 27000000 INFO @ Sun, 02 Jun 2019 19:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.10_summits.bed INFO @ Sun, 02 Jun 2019 19:45:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:45:56: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:45:56: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:45:56: #1 total tags in treatment: 12961623 INFO @ Sun, 02 Jun 2019 19:45:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:45:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:45:57: #1 tags after filtering in treatment: 11029079 INFO @ Sun, 02 Jun 2019 19:45:57: #1 Redundant rate of treatment: 0.15 INFO @ Sun, 02 Jun 2019 19:45:57: #1 finished! INFO @ Sun, 02 Jun 2019 19:45:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:45:58: #2 number of paired peaks: 459 WARNING @ Sun, 02 Jun 2019 19:45:58: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sun, 02 Jun 2019 19:45:58: start model_add_line... INFO @ Sun, 02 Jun 2019 19:45:58: start X-correlation... INFO @ Sun, 02 Jun 2019 19:45:58: end of X-cor INFO @ Sun, 02 Jun 2019 19:45:58: #2 finished! INFO @ Sun, 02 Jun 2019 19:45:58: #2 predicted fragment length is 127 bps INFO @ Sun, 02 Jun 2019 19:45:58: #2 alternative fragment length(s) may be 4,127,142 bps INFO @ Sun, 02 Jun 2019 19:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.05_model.r WARNING @ Sun, 02 Jun 2019 19:45:58: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:45:58: #2 You may need to consider one of the other alternative d(s): 4,127,142 WARNING @ Sun, 02 Jun 2019 19:45:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:45:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:46:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:46:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.20_summits.bed INFO @ Sun, 02 Jun 2019 19:46:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:46:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733161/SRX3733161.05_summits.bed INFO @ Sun, 02 Jun 2019 19:46:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。