Job ID = 2640381 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:02:30 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 : 42,675,204 reads read : 42,675,204 reads written : 42,675,204 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:05 42675204 reads; of these: 42675204 (100.00%) were unpaired; of these: 137094 (0.32%) aligned 0 times 38710900 (90.71%) aligned exactly 1 time 3827210 (8.97%) aligned >1 times 99.68% overall alignment rate Time searching: 00:26:07 Overall time: 00:26:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 672 / 42538110 = 0.0000 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:52:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:52:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:53:01: 1000000 INFO @ Sat, 24 Aug 2019 16:53:09: 2000000 INFO @ Sat, 24 Aug 2019 16:53:17: 3000000 INFO @ Sat, 24 Aug 2019 16:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:53:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:53:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:53:25: 4000000 INFO @ Sat, 24 Aug 2019 16:53:30: 1000000 INFO @ Sat, 24 Aug 2019 16:53:33: 5000000 INFO @ Sat, 24 Aug 2019 16:53:38: 2000000 INFO @ Sat, 24 Aug 2019 16:53:41: 6000000 INFO @ Sat, 24 Aug 2019 16:53:47: 3000000 INFO @ Sat, 24 Aug 2019 16:53:49: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:53:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:53:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:53:55: 4000000 INFO @ Sat, 24 Aug 2019 16:53:57: 8000000 INFO @ Sat, 24 Aug 2019 16:54:00: 1000000 INFO @ Sat, 24 Aug 2019 16:54:03: 5000000 INFO @ Sat, 24 Aug 2019 16:54:05: 9000000 INFO @ Sat, 24 Aug 2019 16:54:08: 2000000 INFO @ Sat, 24 Aug 2019 16:54:11: 6000000 INFO @ Sat, 24 Aug 2019 16:54:14: 10000000 INFO @ Sat, 24 Aug 2019 16:54:17: 3000000 INFO @ Sat, 24 Aug 2019 16:54:20: 7000000 INFO @ Sat, 24 Aug 2019 16:54:23: 11000000 INFO @ Sat, 24 Aug 2019 16:54:25: 4000000 INFO @ Sat, 24 Aug 2019 16:54:28: 8000000 INFO @ Sat, 24 Aug 2019 16:54:31: 12000000 INFO @ Sat, 24 Aug 2019 16:54:33: 5000000 INFO @ Sat, 24 Aug 2019 16:54:36: 9000000 INFO @ Sat, 24 Aug 2019 16:54:39: 13000000 INFO @ Sat, 24 Aug 2019 16:54:41: 6000000 INFO @ Sat, 24 Aug 2019 16:54:45: 10000000 INFO @ Sat, 24 Aug 2019 16:54:48: 14000000 INFO @ Sat, 24 Aug 2019 16:54:49: 7000000 INFO @ Sat, 24 Aug 2019 16:54:53: 11000000 INFO @ Sat, 24 Aug 2019 16:54:56: 15000000 INFO @ Sat, 24 Aug 2019 16:54:58: 8000000 INFO @ Sat, 24 Aug 2019 16:55:01: 12000000 INFO @ Sat, 24 Aug 2019 16:55:04: 16000000 INFO @ Sat, 24 Aug 2019 16:55:06: 9000000 INFO @ Sat, 24 Aug 2019 16:55:09: 13000000 INFO @ Sat, 24 Aug 2019 16:55:12: 17000000 INFO @ Sat, 24 Aug 2019 16:55:14: 10000000 INFO @ Sat, 24 Aug 2019 16:55:18: 14000000 INFO @ Sat, 24 Aug 2019 16:55:20: 18000000 INFO @ Sat, 24 Aug 2019 16:55:23: 11000000 INFO @ Sat, 24 Aug 2019 16:55:26: 15000000 INFO @ Sat, 24 Aug 2019 16:55:28: 19000000 INFO @ Sat, 24 Aug 2019 16:55:31: 12000000 INFO @ Sat, 24 Aug 2019 16:55:34: 16000000 INFO @ Sat, 24 Aug 2019 16:55:36: 20000000 INFO @ Sat, 24 Aug 2019 16:55:39: 13000000 INFO @ Sat, 24 Aug 2019 16:55:43: 17000000 INFO @ Sat, 24 Aug 2019 16:55:47: 21000000 INFO @ Sat, 24 Aug 2019 16:55:48: 14000000 INFO @ Sat, 24 Aug 2019 16:55:51: 18000000 INFO @ Sat, 24 Aug 2019 16:55:56: 15000000 INFO @ Sat, 24 Aug 2019 16:55:57: 22000000 INFO @ Sat, 24 Aug 2019 16:56:00: 19000000 INFO @ Sat, 24 Aug 2019 16:56:04: 16000000 INFO @ Sat, 24 Aug 2019 16:56:06: 23000000 INFO @ Sat, 24 Aug 2019 16:56:10: 20000000 INFO @ Sat, 24 Aug 2019 16:56:13: 17000000 INFO @ Sat, 24 Aug 2019 16:56:14: 24000000 INFO @ Sat, 24 Aug 2019 16:56:19: 21000000 INFO @ Sat, 24 Aug 2019 16:56:22: 18000000 INFO @ Sat, 24 Aug 2019 16:56:23: 25000000 INFO @ Sat, 24 Aug 2019 16:56:28: 22000000 INFO @ Sat, 24 Aug 2019 16:56:30: 19000000 INFO @ Sat, 24 Aug 2019 16:56:32: 26000000 INFO @ Sat, 24 Aug 2019 16:56:37: 23000000 INFO @ Sat, 24 Aug 2019 16:56:40: 20000000 INFO @ Sat, 24 Aug 2019 16:56:41: 27000000 INFO @ Sat, 24 Aug 2019 16:56:47: 24000000 INFO @ Sat, 24 Aug 2019 16:56:49: 21000000 INFO @ Sat, 24 Aug 2019 16:56:50: 28000000 INFO @ Sat, 24 Aug 2019 16:56:56: 25000000 INFO @ Sat, 24 Aug 2019 16:56:58: 22000000 INFO @ Sat, 24 Aug 2019 16:56:58: 29000000 INFO @ Sat, 24 Aug 2019 16:57:05: 26000000 INFO @ Sat, 24 Aug 2019 16:57:07: 23000000 INFO @ Sat, 24 Aug 2019 16:57:08: 30000000 INFO @ Sat, 24 Aug 2019 16:57:15: 27000000 INFO @ Sat, 24 Aug 2019 16:57:17: 24000000 INFO @ Sat, 24 Aug 2019 16:57:19: 31000000 INFO @ Sat, 24 Aug 2019 16:57:24: 28000000 INFO @ Sat, 24 Aug 2019 16:57:26: 25000000 INFO @ Sat, 24 Aug 2019 16:57:28: 32000000 INFO @ Sat, 24 Aug 2019 16:57:33: 29000000 INFO @ Sat, 24 Aug 2019 16:57:36: 26000000 INFO @ Sat, 24 Aug 2019 16:57:36: 33000000 INFO @ Sat, 24 Aug 2019 16:57:42: 30000000 INFO @ Sat, 24 Aug 2019 16:57:44: 34000000 INFO @ Sat, 24 Aug 2019 16:57:45: 27000000 INFO @ Sat, 24 Aug 2019 16:57:52: 31000000 INFO @ Sat, 24 Aug 2019 16:57:52: 35000000 INFO @ Sat, 24 Aug 2019 16:57:54: 28000000 INFO @ Sat, 24 Aug 2019 16:58:00: 36000000 INFO @ Sat, 24 Aug 2019 16:58:01: 32000000 INFO @ Sat, 24 Aug 2019 16:58:03: 29000000 INFO @ Sat, 24 Aug 2019 16:58:09: 37000000 INFO @ Sat, 24 Aug 2019 16:58:10: 33000000 INFO @ Sat, 24 Aug 2019 16:58:12: 30000000 INFO @ Sat, 24 Aug 2019 16:58:17: 38000000 INFO @ Sat, 24 Aug 2019 16:58:20: 34000000 INFO @ Sat, 24 Aug 2019 16:58:22: 31000000 INFO @ Sat, 24 Aug 2019 16:58:26: 39000000 INFO @ Sat, 24 Aug 2019 16:58:29: 35000000 INFO @ Sat, 24 Aug 2019 16:58:31: 32000000 INFO @ Sat, 24 Aug 2019 16:58:37: 40000000 INFO @ Sat, 24 Aug 2019 16:58:38: 36000000 INFO @ Sat, 24 Aug 2019 16:58:41: 33000000 INFO @ Sat, 24 Aug 2019 16:58:47: 37000000 INFO @ Sat, 24 Aug 2019 16:58:48: 41000000 INFO @ Sat, 24 Aug 2019 16:58:50: 34000000 INFO @ Sat, 24 Aug 2019 16:58:56: 38000000 INFO @ Sat, 24 Aug 2019 16:58:59: 35000000 INFO @ Sat, 24 Aug 2019 16:59:00: 42000000 INFO @ Sat, 24 Aug 2019 16:59:05: 39000000 INFO @ Sat, 24 Aug 2019 16:59:07: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 16:59:07: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 16:59:07: #1 total tags in treatment: 42537438 INFO @ Sat, 24 Aug 2019 16:59:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:59:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:59:08: #1 tags after filtering in treatment: 42537315 INFO @ Sat, 24 Aug 2019 16:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:59:08: #1 finished! INFO @ Sat, 24 Aug 2019 16:59:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:59:08: 36000000 INFO @ Sat, 24 Aug 2019 16:59:12: #2 number of paired peaks: 561 WARNING @ Sat, 24 Aug 2019 16:59:12: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 24 Aug 2019 16:59:12: start model_add_line... INFO @ Sat, 24 Aug 2019 16:59:12: start X-correlation... INFO @ Sat, 24 Aug 2019 16:59:12: end of X-cor INFO @ Sat, 24 Aug 2019 16:59:12: #2 finished! INFO @ Sat, 24 Aug 2019 16:59:12: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 16:59:12: #2 alternative fragment length(s) may be 51,568 bps INFO @ Sat, 24 Aug 2019 16:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.05_model.r WARNING @ Sat, 24 Aug 2019 16:59:12: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:59:12: #2 You may need to consider one of the other alternative d(s): 51,568 WARNING @ Sat, 24 Aug 2019 16:59:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:59:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:59:14: 40000000 INFO @ Sat, 24 Aug 2019 16:59:17: 37000000 INFO @ Sat, 24 Aug 2019 16:59:23: 41000000 INFO @ Sat, 24 Aug 2019 16:59:26: 38000000 INFO @ Sat, 24 Aug 2019 16:59:32: 42000000 INFO @ Sat, 24 Aug 2019 16:59:34: 39000000 INFO @ Sat, 24 Aug 2019 16:59:38: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 16:59:38: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 16:59:38: #1 total tags in treatment: 42537438 INFO @ Sat, 24 Aug 2019 16:59:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:59:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:59:39: #1 tags after filtering in treatment: 42537315 INFO @ Sat, 24 Aug 2019 16:59:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:59:39: #1 finished! INFO @ Sat, 24 Aug 2019 16:59:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:59:43: 40000000 INFO @ Sat, 24 Aug 2019 16:59:43: #2 number of paired peaks: 561 WARNING @ Sat, 24 Aug 2019 16:59:43: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 24 Aug 2019 16:59:43: start model_add_line... INFO @ Sat, 24 Aug 2019 16:59:43: start X-correlation... INFO @ Sat, 24 Aug 2019 16:59:43: end of X-cor INFO @ Sat, 24 Aug 2019 16:59:43: #2 finished! INFO @ Sat, 24 Aug 2019 16:59:43: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 16:59:43: #2 alternative fragment length(s) may be 51,568 bps INFO @ Sat, 24 Aug 2019 16:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.10_model.r WARNING @ Sat, 24 Aug 2019 16:59:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:59:43: #2 You may need to consider one of the other alternative d(s): 51,568 WARNING @ Sat, 24 Aug 2019 16:59:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:59:43: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:59:52: 41000000 INFO @ Sat, 24 Aug 2019 17:00:00: 42000000 INFO @ Sat, 24 Aug 2019 17:00:06: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:00:06: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:00:06: #1 total tags in treatment: 42537438 INFO @ Sat, 24 Aug 2019 17:00:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:00:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:00:07: #1 tags after filtering in treatment: 42537315 INFO @ Sat, 24 Aug 2019 17:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:00:07: #1 finished! INFO @ Sat, 24 Aug 2019 17:00:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:00:11: #2 number of paired peaks: 561 WARNING @ Sat, 24 Aug 2019 17:00:11: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 24 Aug 2019 17:00:11: start model_add_line... INFO @ Sat, 24 Aug 2019 17:00:11: start X-correlation... INFO @ Sat, 24 Aug 2019 17:00:11: end of X-cor INFO @ Sat, 24 Aug 2019 17:00:11: #2 finished! INFO @ Sat, 24 Aug 2019 17:00:11: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 17:00:11: #2 alternative fragment length(s) may be 51,568 bps INFO @ Sat, 24 Aug 2019 17:00:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.20_model.r WARNING @ Sat, 24 Aug 2019 17:00:11: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:00:11: #2 You may need to consider one of the other alternative d(s): 51,568 WARNING @ Sat, 24 Aug 2019 17:00:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:00:11: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:00:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:01:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:01:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:02:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.05_summits.bed INFO @ Sat, 24 Aug 2019 17:02:29: Done! pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (651 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.10_summits.bed INFO @ Sat, 24 Aug 2019 17:03:00: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:03:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:03:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2901254/ERX2901254.20_summits.bed INFO @ Sat, 24 Aug 2019 17:03:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (91 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。