Job ID = 2001141 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T18:24:52 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 : 29,290,093 reads read : 29,290,093 reads written : 29,290,093 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:15 29290093 reads; of these: 29290093 (100.00%) were unpaired; of these: 487357 (1.66%) aligned 0 times 19868658 (67.83%) aligned exactly 1 time 8934078 (30.50%) aligned >1 times 98.34% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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 8 files... [bam_rmdupse_core] 523615 / 28802736 = 0.0182 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 @ Fri, 05 Jul 2019 04:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.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 @ Fri, 05 Jul 2019 04:01:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.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 @ Fri, 05 Jul 2019 04:01:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.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 @ Fri, 05 Jul 2019 04:01:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:17: 1000000 INFO @ Fri, 05 Jul 2019 04:01:17: 1000000 INFO @ Fri, 05 Jul 2019 04:01:19: 1000000 INFO @ Fri, 05 Jul 2019 04:01:25: 2000000 INFO @ Fri, 05 Jul 2019 04:01:27: 2000000 INFO @ Fri, 05 Jul 2019 04:01:28: 2000000 INFO @ Fri, 05 Jul 2019 04:01:34: 3000000 INFO @ Fri, 05 Jul 2019 04:01:37: 3000000 INFO @ Fri, 05 Jul 2019 04:01:39: 3000000 INFO @ Fri, 05 Jul 2019 04:01:43: 4000000 INFO @ Fri, 05 Jul 2019 04:01:46: 4000000 INFO @ Fri, 05 Jul 2019 04:01:51: 4000000 INFO @ Fri, 05 Jul 2019 04:01:52: 5000000 INFO @ Fri, 05 Jul 2019 04:01:56: 5000000 INFO @ Fri, 05 Jul 2019 04:02:01: 6000000 INFO @ Fri, 05 Jul 2019 04:02:02: 5000000 INFO @ Fri, 05 Jul 2019 04:02:06: 6000000 INFO @ Fri, 05 Jul 2019 04:02:09: 7000000 INFO @ Fri, 05 Jul 2019 04:02:11: 6000000 INFO @ Fri, 05 Jul 2019 04:02:16: 7000000 INFO @ Fri, 05 Jul 2019 04:02:18: 8000000 INFO @ Fri, 05 Jul 2019 04:02:20: 7000000 INFO @ Fri, 05 Jul 2019 04:02:26: 9000000 INFO @ Fri, 05 Jul 2019 04:02:27: 8000000 INFO @ Fri, 05 Jul 2019 04:02:29: 8000000 INFO @ Fri, 05 Jul 2019 04:02:34: 10000000 INFO @ Fri, 05 Jul 2019 04:02:37: 9000000 INFO @ Fri, 05 Jul 2019 04:02:38: 9000000 INFO @ Fri, 05 Jul 2019 04:02:42: 11000000 INFO @ Fri, 05 Jul 2019 04:02:45: 10000000 INFO @ Fri, 05 Jul 2019 04:02:47: 10000000 INFO @ Fri, 05 Jul 2019 04:02:50: 12000000 INFO @ Fri, 05 Jul 2019 04:02:54: 11000000 INFO @ Fri, 05 Jul 2019 04:02:58: 11000000 INFO @ Fri, 05 Jul 2019 04:02:58: 13000000 INFO @ Fri, 05 Jul 2019 04:03:04: 12000000 INFO @ Fri, 05 Jul 2019 04:03:07: 12000000 INFO @ Fri, 05 Jul 2019 04:03:08: 14000000 INFO @ Fri, 05 Jul 2019 04:03:13: 13000000 INFO @ Fri, 05 Jul 2019 04:03:17: 15000000 INFO @ Fri, 05 Jul 2019 04:03:17: 13000000 INFO @ Fri, 05 Jul 2019 04:03:23: 14000000 INFO @ Fri, 05 Jul 2019 04:03:24: 16000000 INFO @ Fri, 05 Jul 2019 04:03:26: 14000000 INFO @ Fri, 05 Jul 2019 04:03:32: 17000000 INFO @ Fri, 05 Jul 2019 04:03:33: 15000000 INFO @ Fri, 05 Jul 2019 04:03:36: 15000000 INFO @ Fri, 05 Jul 2019 04:03:40: 18000000 INFO @ Fri, 05 Jul 2019 04:03:43: 16000000 INFO @ Fri, 05 Jul 2019 04:03:46: 16000000 INFO @ Fri, 05 Jul 2019 04:03:48: 19000000 INFO @ Fri, 05 Jul 2019 04:03:52: 17000000 INFO @ Fri, 05 Jul 2019 04:03:55: 20000000 INFO @ Fri, 05 Jul 2019 04:03:56: 17000000 INFO @ Fri, 05 Jul 2019 04:04:02: 18000000 INFO @ Fri, 05 Jul 2019 04:04:03: 21000000 INFO @ Fri, 05 Jul 2019 04:04:06: 18000000 INFO @ Fri, 05 Jul 2019 04:04:11: 19000000 INFO @ Fri, 05 Jul 2019 04:04:12: 22000000 INFO @ Fri, 05 Jul 2019 04:04:15: 19000000 INFO @ Fri, 05 Jul 2019 04:04:20: 23000000 INFO @ Fri, 05 Jul 2019 04:04:21: 20000000 INFO @ Fri, 05 Jul 2019 04:04:25: 20000000 INFO @ Fri, 05 Jul 2019 04:04:28: 24000000 INFO @ Fri, 05 Jul 2019 04:04:31: 21000000 INFO @ Fri, 05 Jul 2019 04:04:35: 21000000 INFO @ Fri, 05 Jul 2019 04:04:36: 25000000 INFO @ Fri, 05 Jul 2019 04:04:40: 22000000 INFO @ Fri, 05 Jul 2019 04:04:44: 26000000 INFO @ Fri, 05 Jul 2019 04:04:45: 22000000 INFO @ Fri, 05 Jul 2019 04:04:50: 23000000 INFO @ Fri, 05 Jul 2019 04:04:54: 27000000 INFO @ Fri, 05 Jul 2019 04:04:55: 23000000 INFO @ Fri, 05 Jul 2019 04:04:59: 24000000 INFO @ Fri, 05 Jul 2019 04:05:02: 28000000 INFO @ Fri, 05 Jul 2019 04:05:04: 24000000 INFO @ Fri, 05 Jul 2019 04:05:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:05:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:05:05: #1 total tags in treatment: 28279121 INFO @ Fri, 05 Jul 2019 04:05:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:05:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:05:06: #1 tags after filtering in treatment: 28279030 INFO @ Fri, 05 Jul 2019 04:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:05:06: #1 finished! INFO @ Fri, 05 Jul 2019 04:05:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:05:09: 25000000 INFO @ Fri, 05 Jul 2019 04:05:09: #2 number of paired peaks: 6138 INFO @ Fri, 05 Jul 2019 04:05:09: start model_add_line... INFO @ Fri, 05 Jul 2019 04:05:10: start X-correlation... INFO @ Fri, 05 Jul 2019 04:05:10: end of X-cor INFO @ Fri, 05 Jul 2019 04:05:10: #2 finished! INFO @ Fri, 05 Jul 2019 04:05:10: #2 predicted fragment length is 36 bps INFO @ Fri, 05 Jul 2019 04:05:10: #2 alternative fragment length(s) may be 36,390 bps INFO @ Fri, 05 Jul 2019 04:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.10_model.r WARNING @ Fri, 05 Jul 2019 04:05:10: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 04:05:10: #2 You may need to consider one of the other alternative d(s): 36,390 WARNING @ Fri, 05 Jul 2019 04:05:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 04:05:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:05:14: 25000000 INFO @ Fri, 05 Jul 2019 04:05:19: 26000000 INFO @ Fri, 05 Jul 2019 04:05:24: 26000000 INFO @ Fri, 05 Jul 2019 04:05:28: 27000000 INFO @ Fri, 05 Jul 2019 04:05:34: 27000000 INFO @ Fri, 05 Jul 2019 04:05:38: 28000000 INFO @ Fri, 05 Jul 2019 04:05:41: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:05:41: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:05:41: #1 total tags in treatment: 28279121 INFO @ Fri, 05 Jul 2019 04:05:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:05:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:05:42: #1 tags after filtering in treatment: 28279030 INFO @ Fri, 05 Jul 2019 04:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:05:42: #1 finished! INFO @ Fri, 05 Jul 2019 04:05:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:05:44: 28000000 INFO @ Fri, 05 Jul 2019 04:05:46: #2 number of paired peaks: 6138 INFO @ Fri, 05 Jul 2019 04:05:46: start model_add_line... INFO @ Fri, 05 Jul 2019 04:05:46: start X-correlation... INFO @ Fri, 05 Jul 2019 04:05:46: end of X-cor INFO @ Fri, 05 Jul 2019 04:05:46: #2 finished! INFO @ Fri, 05 Jul 2019 04:05:46: #2 predicted fragment length is 36 bps INFO @ Fri, 05 Jul 2019 04:05:46: #2 alternative fragment length(s) may be 36,390 bps INFO @ Fri, 05 Jul 2019 04:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.20_model.r WARNING @ Fri, 05 Jul 2019 04:05:46: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 04:05:46: #2 You may need to consider one of the other alternative d(s): 36,390 WARNING @ Fri, 05 Jul 2019 04:05:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 04:05:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:05:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:05:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:05:47: #1 total tags in treatment: 28279121 INFO @ Fri, 05 Jul 2019 04:05:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:05:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:05:47: #1 tags after filtering in treatment: 28279030 INFO @ Fri, 05 Jul 2019 04:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:05:47: #1 finished! INFO @ Fri, 05 Jul 2019 04:05:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:05:51: #2 number of paired peaks: 6138 INFO @ Fri, 05 Jul 2019 04:05:51: start model_add_line... INFO @ Fri, 05 Jul 2019 04:05:51: start X-correlation... INFO @ Fri, 05 Jul 2019 04:05:51: end of X-cor INFO @ Fri, 05 Jul 2019 04:05:51: #2 finished! INFO @ Fri, 05 Jul 2019 04:05:51: #2 predicted fragment length is 36 bps INFO @ Fri, 05 Jul 2019 04:05:51: #2 alternative fragment length(s) may be 36,390 bps INFO @ Fri, 05 Jul 2019 04:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.05_model.r WARNING @ Fri, 05 Jul 2019 04:05:52: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 04:05:52: #2 You may need to consider one of the other alternative d(s): 36,390 WARNING @ Fri, 05 Jul 2019 04:05:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 04:05:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:06:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:07:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:07:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:07:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:07:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:07:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.10_summits.bed INFO @ Fri, 05 Jul 2019 04:07:37: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (1110 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.20_summits.bed INFO @ Fri, 05 Jul 2019 04:08:14: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (494 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:08:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:08:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:08:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX032776/ERX032776.05_summits.bed INFO @ Fri, 05 Jul 2019 04:08:18: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (2091 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。