Job ID = 2640429 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:42:36 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 ) 2019-08-24T07:42:36 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 ) 2019-08-24T07:42:36 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 ) 2019-08-24T07:43:18 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 ) 2019-08-24T07:47:57 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 : 150,360,864 reads read : 150,360,864 reads written : 150,360,864 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR980346.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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 04:18:57 150360864 reads; of these: 150360864 (100.00%) were unpaired; of these: 21075022 (14.02%) aligned 0 times 103790873 (69.03%) aligned exactly 1 time 25494969 (16.96%) aligned >1 times 85.98% overall alignment rate Time searching: 04:19:00 Overall time: 04:19:00 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 56 files... [bam_rmdupse_core] 111066161 / 129285842 = 0.8591 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.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 21:36:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:36:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:36:44: 1000000 INFO @ Sat, 24 Aug 2019 21:36:52: 2000000 INFO @ Sat, 24 Aug 2019 21:37:00: 3000000 INFO @ Sat, 24 Aug 2019 21:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.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 21:37:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:37:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:37:08: 4000000 INFO @ Sat, 24 Aug 2019 21:37:13: 1000000 INFO @ Sat, 24 Aug 2019 21:37:15: 5000000 INFO @ Sat, 24 Aug 2019 21:37:21: 2000000 INFO @ Sat, 24 Aug 2019 21:37:23: 6000000 INFO @ Sat, 24 Aug 2019 21:37:29: 3000000 INFO @ Sat, 24 Aug 2019 21:37:31: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.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 21:37:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:37:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:37:37: 4000000 INFO @ Sat, 24 Aug 2019 21:37:39: 8000000 INFO @ Sat, 24 Aug 2019 21:37:41: 1000000 INFO @ Sat, 24 Aug 2019 21:37:45: 5000000 INFO @ Sat, 24 Aug 2019 21:37:47: 9000000 INFO @ Sat, 24 Aug 2019 21:37:48: 2000000 INFO @ Sat, 24 Aug 2019 21:37:53: 6000000 INFO @ Sat, 24 Aug 2019 21:37:55: 3000000 INFO @ Sat, 24 Aug 2019 21:37:55: 10000000 INFO @ Sat, 24 Aug 2019 21:38:01: 7000000 INFO @ Sat, 24 Aug 2019 21:38:01: 4000000 INFO @ Sat, 24 Aug 2019 21:38:03: 11000000 INFO @ Sat, 24 Aug 2019 21:38:08: 5000000 INFO @ Sat, 24 Aug 2019 21:38:09: 8000000 INFO @ Sat, 24 Aug 2019 21:38:11: 12000000 INFO @ Sat, 24 Aug 2019 21:38:15: 6000000 INFO @ Sat, 24 Aug 2019 21:38:17: 9000000 INFO @ Sat, 24 Aug 2019 21:38:18: 13000000 INFO @ Sat, 24 Aug 2019 21:38:22: 7000000 INFO @ Sat, 24 Aug 2019 21:38:25: 10000000 INFO @ Sat, 24 Aug 2019 21:38:25: 14000000 INFO @ Sat, 24 Aug 2019 21:38:29: 8000000 INFO @ Sat, 24 Aug 2019 21:38:32: 15000000 INFO @ Sat, 24 Aug 2019 21:38:33: 11000000 INFO @ Sat, 24 Aug 2019 21:38:37: 9000000 INFO @ Sat, 24 Aug 2019 21:38:39: 16000000 INFO @ Sat, 24 Aug 2019 21:38:41: 12000000 INFO @ Sat, 24 Aug 2019 21:38:44: 10000000 INFO @ Sat, 24 Aug 2019 21:38:46: 17000000 INFO @ Sat, 24 Aug 2019 21:38:49: 13000000 INFO @ Sat, 24 Aug 2019 21:38:51: 11000000 INFO @ Sat, 24 Aug 2019 21:38:54: 18000000 INFO @ Sat, 24 Aug 2019 21:38:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:38:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:38:56: #1 total tags in treatment: 18219681 INFO @ Sat, 24 Aug 2019 21:38:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:38:56: #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 21:38:56: #1 tags after filtering in treatment: 18219542 INFO @ Sat, 24 Aug 2019 21:38:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:38:56: #1 finished! INFO @ Sat, 24 Aug 2019 21:38:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:38:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:38:57: 14000000 INFO @ Sat, 24 Aug 2019 21:38:58: 12000000 INFO @ Sat, 24 Aug 2019 21:39:01: #2 number of paired peaks: 56528 INFO @ Sat, 24 Aug 2019 21:39:01: start model_add_line... INFO @ Sat, 24 Aug 2019 21:39:01: start X-correlation... INFO @ Sat, 24 Aug 2019 21:39:01: end of X-cor INFO @ Sat, 24 Aug 2019 21:39:01: #2 finished! INFO @ Sat, 24 Aug 2019 21:39:01: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 21:39:01: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 21:39:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.05_model.r WARNING @ Sat, 24 Aug 2019 21:39:01: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:39:01: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 24 Aug 2019 21:39:01: #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 21:39:01: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:39:04: 15000000 INFO @ Sat, 24 Aug 2019 21:39:05: 13000000 INFO @ Sat, 24 Aug 2019 21:39:11: 14000000 INFO @ Sat, 24 Aug 2019 21:39:12: 16000000 INFO @ Sat, 24 Aug 2019 21:39:18: 15000000 INFO @ Sat, 24 Aug 2019 21:39:19: 17000000 INFO @ Sat, 24 Aug 2019 21:39:24: 16000000 INFO @ Sat, 24 Aug 2019 21:39:27: 18000000 INFO @ Sat, 24 Aug 2019 21:39:29: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:39:29: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:39:29: #1 total tags in treatment: 18219681 INFO @ Sat, 24 Aug 2019 21:39:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:39:29: #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 21:39:30: #1 tags after filtering in treatment: 18219542 INFO @ Sat, 24 Aug 2019 21:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:39:30: #1 finished! INFO @ Sat, 24 Aug 2019 21:39:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:39:31: 17000000 INFO @ Sat, 24 Aug 2019 21:39:34: #2 number of paired peaks: 56528 INFO @ Sat, 24 Aug 2019 21:39:34: start model_add_line... INFO @ Sat, 24 Aug 2019 21:39:34: start X-correlation... INFO @ Sat, 24 Aug 2019 21:39:34: end of X-cor INFO @ Sat, 24 Aug 2019 21:39:34: #2 finished! INFO @ Sat, 24 Aug 2019 21:39:34: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 21:39:34: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 21:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.10_model.r WARNING @ Sat, 24 Aug 2019 21:39:34: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:39:34: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 24 Aug 2019 21:39:34: #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 21:39:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:39:38: 18000000 INFO @ Sat, 24 Aug 2019 21:39:39: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:39:39: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:39:39: #1 total tags in treatment: 18219681 INFO @ Sat, 24 Aug 2019 21:39:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:39:39: #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 21:39:40: #1 tags after filtering in treatment: 18219542 INFO @ Sat, 24 Aug 2019 21:39:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:39:40: #1 finished! INFO @ Sat, 24 Aug 2019 21:39:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:39:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:39:44: #2 number of paired peaks: 56528 INFO @ Sat, 24 Aug 2019 21:39:44: start model_add_line... INFO @ Sat, 24 Aug 2019 21:39:45: start X-correlation... INFO @ Sat, 24 Aug 2019 21:39:45: end of X-cor INFO @ Sat, 24 Aug 2019 21:39:45: #2 finished! INFO @ Sat, 24 Aug 2019 21:39:45: #2 predicted fragment length is 87 bps INFO @ Sat, 24 Aug 2019 21:39:45: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 24 Aug 2019 21:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.20_model.r WARNING @ Sat, 24 Aug 2019 21:39:45: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:39:45: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 24 Aug 2019 21:39:45: #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 21:39:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:40:00: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:40:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.05_summits.bed INFO @ Sat, 24 Aug 2019 21:40:31: Done! pass1 - making usageList (211 chroms): 17 millis pass2 - checking and writing primary data (52918 records, 4 fields): 71 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:40:32: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:40:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.10_summits.bed INFO @ Sat, 24 Aug 2019 21:41:01: Done! pass1 - making usageList (155 chroms): 8 millis pass2 - checking and writing primary data (25981 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349434/SRX349434.20_summits.bed INFO @ Sat, 24 Aug 2019 21:41:12: Done! pass1 - making usageList (93 chroms): 4 millis pass2 - checking and writing primary data (9714 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。