Job ID = 2002159 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T01:37:19 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 ) 2019-07-05T01:40:20 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 ) 2019-07-05T01:53:22 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:30 29290093 reads; of these: 29290093 (100.00%) were unpaired; of these: 487463 (1.66%) aligned 0 times 19868470 (67.83%) aligned exactly 1 time 8934160 (30.50%) aligned >1 times 98.34% overall alignment rate Time searching: 00:12:33 Overall time: 00:12:33 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] 523758 / 28802630 = 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 11:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.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 11:25:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:25:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:25:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.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 11:25:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:25:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.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 11:26:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:26:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:26:05: 1000000 INFO @ Fri, 05 Jul 2019 11:26:07: 1000000 INFO @ Fri, 05 Jul 2019 11:26:07: 1000000 INFO @ Fri, 05 Jul 2019 11:26:12: 2000000 INFO @ Fri, 05 Jul 2019 11:26:15: 2000000 INFO @ Fri, 05 Jul 2019 11:26:15: 2000000 INFO @ Fri, 05 Jul 2019 11:26:20: 3000000 INFO @ Fri, 05 Jul 2019 11:26:22: 3000000 INFO @ Fri, 05 Jul 2019 11:26:24: 3000000 INFO @ Fri, 05 Jul 2019 11:26:27: 4000000 INFO @ Fri, 05 Jul 2019 11:26:30: 4000000 INFO @ Fri, 05 Jul 2019 11:26:32: 4000000 INFO @ Fri, 05 Jul 2019 11:26:34: 5000000 INFO @ Fri, 05 Jul 2019 11:26:37: 5000000 INFO @ Fri, 05 Jul 2019 11:26:40: 5000000 INFO @ Fri, 05 Jul 2019 11:26:42: 6000000 INFO @ Fri, 05 Jul 2019 11:26:44: 6000000 INFO @ Fri, 05 Jul 2019 11:26:48: 6000000 INFO @ Fri, 05 Jul 2019 11:26:49: 7000000 INFO @ Fri, 05 Jul 2019 11:26:52: 7000000 INFO @ Fri, 05 Jul 2019 11:26:56: 8000000 INFO @ Fri, 05 Jul 2019 11:26:56: 7000000 INFO @ Fri, 05 Jul 2019 11:26:59: 8000000 INFO @ Fri, 05 Jul 2019 11:27:03: 9000000 INFO @ Fri, 05 Jul 2019 11:27:04: 8000000 INFO @ Fri, 05 Jul 2019 11:27:06: 9000000 INFO @ Fri, 05 Jul 2019 11:27:10: 10000000 INFO @ Fri, 05 Jul 2019 11:27:12: 9000000 INFO @ Fri, 05 Jul 2019 11:27:13: 10000000 INFO @ Fri, 05 Jul 2019 11:27:18: 11000000 INFO @ Fri, 05 Jul 2019 11:27:20: 10000000 INFO @ Fri, 05 Jul 2019 11:27:20: 11000000 INFO @ Fri, 05 Jul 2019 11:27:25: 12000000 INFO @ Fri, 05 Jul 2019 11:27:28: 12000000 INFO @ Fri, 05 Jul 2019 11:27:28: 11000000 INFO @ Fri, 05 Jul 2019 11:27:32: 13000000 INFO @ Fri, 05 Jul 2019 11:27:35: 13000000 INFO @ Fri, 05 Jul 2019 11:27:36: 12000000 INFO @ Fri, 05 Jul 2019 11:27:39: 14000000 INFO @ Fri, 05 Jul 2019 11:27:42: 14000000 INFO @ Fri, 05 Jul 2019 11:27:44: 13000000 INFO @ Fri, 05 Jul 2019 11:27:46: 15000000 INFO @ Fri, 05 Jul 2019 11:27:49: 15000000 INFO @ Fri, 05 Jul 2019 11:27:52: 14000000 INFO @ Fri, 05 Jul 2019 11:27:54: 16000000 INFO @ Fri, 05 Jul 2019 11:27:57: 16000000 INFO @ Fri, 05 Jul 2019 11:27:59: 15000000 INFO @ Fri, 05 Jul 2019 11:28:01: 17000000 INFO @ Fri, 05 Jul 2019 11:28:04: 17000000 INFO @ Fri, 05 Jul 2019 11:28:07: 16000000 INFO @ Fri, 05 Jul 2019 11:28:08: 18000000 INFO @ Fri, 05 Jul 2019 11:28:11: 18000000 INFO @ Fri, 05 Jul 2019 11:28:15: 17000000 INFO @ Fri, 05 Jul 2019 11:28:16: 19000000 INFO @ Fri, 05 Jul 2019 11:28:18: 19000000 INFO @ Fri, 05 Jul 2019 11:28:23: 20000000 INFO @ Fri, 05 Jul 2019 11:28:23: 18000000 INFO @ Fri, 05 Jul 2019 11:28:26: 20000000 INFO @ Fri, 05 Jul 2019 11:28:30: 21000000 INFO @ Fri, 05 Jul 2019 11:28:31: 19000000 INFO @ Fri, 05 Jul 2019 11:28:33: 21000000 INFO @ Fri, 05 Jul 2019 11:28:37: 22000000 INFO @ Fri, 05 Jul 2019 11:28:39: 20000000 INFO @ Fri, 05 Jul 2019 11:28:40: 22000000 INFO @ Fri, 05 Jul 2019 11:28:45: 23000000 INFO @ Fri, 05 Jul 2019 11:28:47: 23000000 INFO @ Fri, 05 Jul 2019 11:28:48: 21000000 INFO @ Fri, 05 Jul 2019 11:28:52: 24000000 INFO @ Fri, 05 Jul 2019 11:28:55: 24000000 INFO @ Fri, 05 Jul 2019 11:28:56: 22000000 INFO @ Fri, 05 Jul 2019 11:28:59: 25000000 INFO @ Fri, 05 Jul 2019 11:29:02: 25000000 INFO @ Fri, 05 Jul 2019 11:29:03: 23000000 INFO @ Fri, 05 Jul 2019 11:29:06: 26000000 INFO @ Fri, 05 Jul 2019 11:29:09: 26000000 INFO @ Fri, 05 Jul 2019 11:29:11: 24000000 INFO @ Fri, 05 Jul 2019 11:29:14: 27000000 INFO @ Fri, 05 Jul 2019 11:29:17: 27000000 INFO @ Fri, 05 Jul 2019 11:29:19: 25000000 INFO @ Fri, 05 Jul 2019 11:29:21: 28000000 INFO @ Fri, 05 Jul 2019 11:29:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:29:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:29:24: #1 total tags in treatment: 28278872 INFO @ Fri, 05 Jul 2019 11:29:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:29:24: #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 11:29:24: 28000000 INFO @ Fri, 05 Jul 2019 11:29:24: #1 tags after filtering in treatment: 28278785 INFO @ Fri, 05 Jul 2019 11:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:29:24: #1 finished! INFO @ Fri, 05 Jul 2019 11:29:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:29:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:29:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:29:26: #1 total tags in treatment: 28278872 INFO @ Fri, 05 Jul 2019 11:29:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:29:26: #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 11:29:27: 26000000 INFO @ Fri, 05 Jul 2019 11:29:27: #1 tags after filtering in treatment: 28278785 INFO @ Fri, 05 Jul 2019 11:29:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:29:27: #1 finished! INFO @ Fri, 05 Jul 2019 11:29:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:29:28: #2 number of paired peaks: 6133 INFO @ Fri, 05 Jul 2019 11:29:28: start model_add_line... INFO @ Fri, 05 Jul 2019 11:29:28: start X-correlation... INFO @ Fri, 05 Jul 2019 11:29:28: end of X-cor INFO @ Fri, 05 Jul 2019 11:29:28: #2 finished! INFO @ Fri, 05 Jul 2019 11:29:28: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 11:29:28: #2 alternative fragment length(s) may be 37,385,591 bps INFO @ Fri, 05 Jul 2019 11:29:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.05_model.r WARNING @ Fri, 05 Jul 2019 11:29:28: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:29:28: #2 You may need to consider one of the other alternative d(s): 37,385,591 WARNING @ Fri, 05 Jul 2019 11:29:28: #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 11:29:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:29:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:29:30: #2 number of paired peaks: 6133 INFO @ Fri, 05 Jul 2019 11:29:30: start model_add_line... INFO @ Fri, 05 Jul 2019 11:29:31: start X-correlation... INFO @ Fri, 05 Jul 2019 11:29:31: end of X-cor INFO @ Fri, 05 Jul 2019 11:29:31: #2 finished! INFO @ Fri, 05 Jul 2019 11:29:31: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 11:29:31: #2 alternative fragment length(s) may be 37,385,591 bps INFO @ Fri, 05 Jul 2019 11:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.20_model.r WARNING @ Fri, 05 Jul 2019 11:29:31: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:29:31: #2 You may need to consider one of the other alternative d(s): 37,385,591 WARNING @ Fri, 05 Jul 2019 11:29:31: #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 11:29:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:29:35: 27000000 INFO @ Fri, 05 Jul 2019 11:29:42: 28000000 INFO @ Fri, 05 Jul 2019 11:29:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:29:48: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:29:48: #1 total tags in treatment: 28278872 INFO @ Fri, 05 Jul 2019 11:29:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:29:48: #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 11:29:49: #1 tags after filtering in treatment: 28278785 INFO @ Fri, 05 Jul 2019 11:29:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:29:49: #1 finished! INFO @ Fri, 05 Jul 2019 11:29:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:29:52: #2 number of paired peaks: 6133 INFO @ Fri, 05 Jul 2019 11:29:52: start model_add_line... INFO @ Fri, 05 Jul 2019 11:29:52: start X-correlation... INFO @ Fri, 05 Jul 2019 11:29:52: end of X-cor INFO @ Fri, 05 Jul 2019 11:29:52: #2 finished! INFO @ Fri, 05 Jul 2019 11:29:52: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 11:29:52: #2 alternative fragment length(s) may be 37,385,591 bps INFO @ Fri, 05 Jul 2019 11:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.10_model.r WARNING @ Fri, 05 Jul 2019 11:29:52: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:29:52: #2 You may need to consider one of the other alternative d(s): 37,385,591 WARNING @ Fri, 05 Jul 2019 11:29:52: #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 11:29:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:30:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:30:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:31:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.05_summits.bed INFO @ Fri, 05 Jul 2019 11:31:39: Done! pass1 - making usageList (51 chroms): 3 millis pass2 - checking and writing primary data (2073 records, 4 fields): 12 millis INFO @ Fri, 05 Jul 2019 11:31:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:31:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:31:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.20_summits.bed INFO @ Fri, 05 Jul 2019 11:31:42: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (482 records, 4 fields): 223 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190363/ERX190363.10_summits.bed INFO @ Fri, 05 Jul 2019 11:32:03: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1098 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。