Job ID = 2640427 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:40:54 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 ) 2019-08-24T07:41:02 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 ) 2019-08-24T07:41:02 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 ) 2019-08-24T07:43:31 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 ) 2019-08-24T07:45:25 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 ) 2019-08-24T07:47:30 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 158,941,694 reads read : 158,941,694 reads written : 158,941,694 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR980344.sra.cache’: 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: 04:09:10 158941694 reads; of these: 158941694 (100.00%) were unpaired; of these: 41389623 (26.04%) aligned 0 times 99475377 (62.59%) aligned exactly 1 time 18076694 (11.37%) aligned >1 times 73.96% overall alignment rate Time searching: 04:09:13 Overall time: 04:09:13 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 48 files... [bam_rmdupse_core] 95424492 / 117552071 = 0.8118 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.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 21:24:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:24:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:24:34: 1000000 INFO @ Sat, 24 Aug 2019 21:24:42: 2000000 INFO @ Sat, 24 Aug 2019 21:24:50: 3000000 INFO @ Sat, 24 Aug 2019 21:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.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 21:24:55: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:24:55: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:24:59: 4000000 INFO @ Sat, 24 Aug 2019 21:25:03: 1000000 INFO @ Sat, 24 Aug 2019 21:25:07: 5000000 INFO @ Sat, 24 Aug 2019 21:25:12: 2000000 INFO @ Sat, 24 Aug 2019 21:25:15: 6000000 INFO @ Sat, 24 Aug 2019 21:25:20: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:25:24: 7000000 INFO @ Sat, 24 Aug 2019 21:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.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 21:25:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:25:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:25:29: 4000000 INFO @ Sat, 24 Aug 2019 21:25:33: 8000000 INFO @ Sat, 24 Aug 2019 21:25:34: 1000000 INFO @ Sat, 24 Aug 2019 21:25:38: 5000000 INFO @ Sat, 24 Aug 2019 21:25:41: 2000000 INFO @ Sat, 24 Aug 2019 21:25:42: 9000000 INFO @ Sat, 24 Aug 2019 21:25:47: 6000000 INFO @ Sat, 24 Aug 2019 21:25:49: 3000000 INFO @ Sat, 24 Aug 2019 21:25:50: 10000000 INFO @ Sat, 24 Aug 2019 21:25:56: 7000000 INFO @ Sat, 24 Aug 2019 21:25:57: 4000000 INFO @ Sat, 24 Aug 2019 21:25:59: 11000000 INFO @ Sat, 24 Aug 2019 21:26:04: 5000000 INFO @ Sat, 24 Aug 2019 21:26:06: 8000000 INFO @ Sat, 24 Aug 2019 21:26:08: 12000000 INFO @ Sat, 24 Aug 2019 21:26:12: 6000000 INFO @ Sat, 24 Aug 2019 21:26:14: 9000000 INFO @ Sat, 24 Aug 2019 21:26:17: 13000000 INFO @ Sat, 24 Aug 2019 21:26:19: 7000000 INFO @ Sat, 24 Aug 2019 21:26:23: 10000000 INFO @ Sat, 24 Aug 2019 21:26:26: 14000000 INFO @ Sat, 24 Aug 2019 21:26:27: 8000000 INFO @ Sat, 24 Aug 2019 21:26:32: 11000000 INFO @ Sat, 24 Aug 2019 21:26:34: 9000000 INFO @ Sat, 24 Aug 2019 21:26:34: 15000000 INFO @ Sat, 24 Aug 2019 21:26:41: 12000000 INFO @ Sat, 24 Aug 2019 21:26:42: 10000000 INFO @ Sat, 24 Aug 2019 21:26:43: 16000000 INFO @ Sat, 24 Aug 2019 21:26:49: 11000000 INFO @ Sat, 24 Aug 2019 21:26:50: 13000000 INFO @ Sat, 24 Aug 2019 21:26:52: 17000000 INFO @ Sat, 24 Aug 2019 21:26:57: 12000000 INFO @ Sat, 24 Aug 2019 21:26:59: 14000000 INFO @ Sat, 24 Aug 2019 21:27:01: 18000000 INFO @ Sat, 24 Aug 2019 21:27:04: 13000000 INFO @ Sat, 24 Aug 2019 21:27:08: 15000000 INFO @ Sat, 24 Aug 2019 21:27:10: 19000000 INFO @ Sat, 24 Aug 2019 21:27:11: 14000000 INFO @ Sat, 24 Aug 2019 21:27:17: 16000000 INFO @ Sat, 24 Aug 2019 21:27:19: 15000000 INFO @ Sat, 24 Aug 2019 21:27:19: 20000000 INFO @ Sat, 24 Aug 2019 21:27:26: 17000000 INFO @ Sat, 24 Aug 2019 21:27:26: 16000000 INFO @ Sat, 24 Aug 2019 21:27:28: 21000000 INFO @ Sat, 24 Aug 2019 21:27:34: 17000000 INFO @ Sat, 24 Aug 2019 21:27:34: 18000000 INFO @ Sat, 24 Aug 2019 21:27:37: 22000000 INFO @ Sat, 24 Aug 2019 21:27:38: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:27:38: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:27:38: #1 total tags in treatment: 22127579 INFO @ Sat, 24 Aug 2019 21:27:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:27:38: #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 21:27:39: #1 tags after filtering in treatment: 22127428 INFO @ Sat, 24 Aug 2019 21:27:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:27:39: #1 finished! INFO @ Sat, 24 Aug 2019 21:27:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:27:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:27:41: 18000000 INFO @ Sat, 24 Aug 2019 21:27:43: 19000000 INFO @ Sat, 24 Aug 2019 21:27:45: #2 number of paired peaks: 80802 INFO @ Sat, 24 Aug 2019 21:27:45: start model_add_line... INFO @ Sat, 24 Aug 2019 21:27:45: start X-correlation... INFO @ Sat, 24 Aug 2019 21:27:45: end of X-cor INFO @ Sat, 24 Aug 2019 21:27:45: #2 finished! INFO @ Sat, 24 Aug 2019 21:27:45: #2 predicted fragment length is 76 bps INFO @ Sat, 24 Aug 2019 21:27:45: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 24 Aug 2019 21:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.05_model.r WARNING @ Sat, 24 Aug 2019 21:27:45: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:27:45: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 24 Aug 2019 21:27:45: #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 21:27:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:27:48: 19000000 INFO @ Sat, 24 Aug 2019 21:27:51: 20000000 INFO @ Sat, 24 Aug 2019 21:27:56: 20000000 INFO @ Sat, 24 Aug 2019 21:27:59: 21000000 INFO @ Sat, 24 Aug 2019 21:28:03: 21000000 INFO @ Sat, 24 Aug 2019 21:28:08: 22000000 INFO @ Sat, 24 Aug 2019 21:28:09: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:28:09: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:28:09: #1 total tags in treatment: 22127579 INFO @ Sat, 24 Aug 2019 21:28:09: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:28:09: #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 21:28:09: #1 tags after filtering in treatment: 22127428 INFO @ Sat, 24 Aug 2019 21:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:28:09: #1 finished! INFO @ Sat, 24 Aug 2019 21:28:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:28:11: 22000000 INFO @ Sat, 24 Aug 2019 21:28:12: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:28:12: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:28:12: #1 total tags in treatment: 22127579 INFO @ Sat, 24 Aug 2019 21:28:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:28:12: #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 21:28:12: #1 tags after filtering in treatment: 22127428 INFO @ Sat, 24 Aug 2019 21:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:28:12: #1 finished! INFO @ Sat, 24 Aug 2019 21:28:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:28:15: #2 number of paired peaks: 80802 INFO @ Sat, 24 Aug 2019 21:28:15: start model_add_line... INFO @ Sat, 24 Aug 2019 21:28:16: start X-correlation... INFO @ Sat, 24 Aug 2019 21:28:16: end of X-cor INFO @ Sat, 24 Aug 2019 21:28:16: #2 finished! INFO @ Sat, 24 Aug 2019 21:28:16: #2 predicted fragment length is 76 bps INFO @ Sat, 24 Aug 2019 21:28:16: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 24 Aug 2019 21:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.10_model.r WARNING @ Sat, 24 Aug 2019 21:28:16: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:28:16: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 24 Aug 2019 21:28:16: #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 21:28:16: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:28:18: #2 number of paired peaks: 80802 INFO @ Sat, 24 Aug 2019 21:28:18: start model_add_line... INFO @ Sat, 24 Aug 2019 21:28:19: start X-correlation... INFO @ Sat, 24 Aug 2019 21:28:19: end of X-cor INFO @ Sat, 24 Aug 2019 21:28:19: #2 finished! INFO @ Sat, 24 Aug 2019 21:28:19: #2 predicted fragment length is 76 bps INFO @ Sat, 24 Aug 2019 21:28:19: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 24 Aug 2019 21:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.20_model.r WARNING @ Sat, 24 Aug 2019 21:28:19: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:28:19: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 24 Aug 2019 21:28:19: #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 21:28:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:28:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:29:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:29:26: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:29:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.05_summits.bed INFO @ Sat, 24 Aug 2019 21:29:34: Done! pass1 - making usageList (242 chroms): 24 millis pass2 - checking and writing primary data (95336 records, 4 fields): 127 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.10_summits.bed INFO @ Sat, 24 Aug 2019 21:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349432/SRX349432.20_summits.bed INFO @ Sat, 24 Aug 2019 21:30:03: Done! INFO @ Sat, 24 Aug 2019 21:30:03: Done! pass1 - making usageList (139 chroms): 17 millis pass2 - checking and writing primary data (41092 records, 4 fields): 60 millis CompletedMACS2peakCalling pass1 - making usageList (198 chroms): 17 millis pass2 - checking and writing primary data (65464 records, 4 fields): 87 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。