Job ID = 2640406 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:09:59 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 ) 2019-08-24T07:09:59 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 ) 2019-08-24T07:09:59 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 ) 2019-08-24T07:10:00 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 ) 2019-08-24T07:10:00 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 ) 2019-08-24T07:10:00 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 : 26,786,620 reads read : 26,786,620 reads written : 26,786,620 spots read : 25,916,055 reads read : 25,916,055 reads written : 25,916,055 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR060849.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR060850.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: 00:16:10 52702675 reads; of these: 52702675 (100.00%) were unpaired; of these: 23796965 (45.15%) aligned 0 times 18964942 (35.98%) aligned exactly 1 time 9940768 (18.86%) aligned >1 times 54.85% overall alignment rate Time searching: 00:16:13 Overall time: 00:16:13 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 8 files... [bam_rmdupse_core] 3264268 / 28905710 = 0.1129 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.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 16:39:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:39:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:39:14: 1000000 INFO @ Sat, 24 Aug 2019 16:39:21: 2000000 INFO @ Sat, 24 Aug 2019 16:39:29: 3000000 INFO @ Sat, 24 Aug 2019 16:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.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 16:39:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:39:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:39:36: 4000000 INFO @ Sat, 24 Aug 2019 16:39:43: 1000000 INFO @ Sat, 24 Aug 2019 16:39:44: 5000000 INFO @ Sat, 24 Aug 2019 16:39:50: 2000000 INFO @ Sat, 24 Aug 2019 16:39:52: 6000000 INFO @ Sat, 24 Aug 2019 16:39:57: 3000000 INFO @ Sat, 24 Aug 2019 16:40:00: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:40:04: 4000000 INFO @ Sat, 24 Aug 2019 16:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.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 16:40:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:40:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:40:07: 8000000 INFO @ Sat, 24 Aug 2019 16:40:11: 5000000 INFO @ Sat, 24 Aug 2019 16:40:15: 9000000 INFO @ Sat, 24 Aug 2019 16:40:15: 1000000 INFO @ Sat, 24 Aug 2019 16:40:19: 6000000 INFO @ Sat, 24 Aug 2019 16:40:23: 10000000 INFO @ Sat, 24 Aug 2019 16:40:24: 2000000 INFO @ Sat, 24 Aug 2019 16:40:26: 7000000 INFO @ Sat, 24 Aug 2019 16:40:30: 11000000 INFO @ Sat, 24 Aug 2019 16:40:33: 3000000 INFO @ Sat, 24 Aug 2019 16:40:33: 8000000 INFO @ Sat, 24 Aug 2019 16:40:38: 12000000 INFO @ Sat, 24 Aug 2019 16:40:40: 9000000 INFO @ Sat, 24 Aug 2019 16:40:42: 4000000 INFO @ Sat, 24 Aug 2019 16:40:45: 13000000 INFO @ Sat, 24 Aug 2019 16:40:47: 10000000 INFO @ Sat, 24 Aug 2019 16:40:50: 5000000 INFO @ Sat, 24 Aug 2019 16:40:53: 14000000 INFO @ Sat, 24 Aug 2019 16:40:54: 11000000 INFO @ Sat, 24 Aug 2019 16:40:59: 6000000 INFO @ Sat, 24 Aug 2019 16:41:01: 15000000 INFO @ Sat, 24 Aug 2019 16:41:01: 12000000 INFO @ Sat, 24 Aug 2019 16:41:08: 7000000 INFO @ Sat, 24 Aug 2019 16:41:08: 13000000 INFO @ Sat, 24 Aug 2019 16:41:08: 16000000 INFO @ Sat, 24 Aug 2019 16:41:15: 14000000 INFO @ Sat, 24 Aug 2019 16:41:16: 17000000 INFO @ Sat, 24 Aug 2019 16:41:17: 8000000 INFO @ Sat, 24 Aug 2019 16:41:22: 15000000 INFO @ Sat, 24 Aug 2019 16:41:23: 18000000 INFO @ Sat, 24 Aug 2019 16:41:26: 9000000 INFO @ Sat, 24 Aug 2019 16:41:29: 16000000 INFO @ Sat, 24 Aug 2019 16:41:31: 19000000 INFO @ Sat, 24 Aug 2019 16:41:35: 10000000 INFO @ Sat, 24 Aug 2019 16:41:36: 17000000 INFO @ Sat, 24 Aug 2019 16:41:38: 20000000 INFO @ Sat, 24 Aug 2019 16:41:43: 18000000 INFO @ Sat, 24 Aug 2019 16:41:44: 11000000 INFO @ Sat, 24 Aug 2019 16:41:46: 21000000 INFO @ Sat, 24 Aug 2019 16:41:50: 19000000 INFO @ Sat, 24 Aug 2019 16:41:53: 12000000 INFO @ Sat, 24 Aug 2019 16:41:53: 22000000 INFO @ Sat, 24 Aug 2019 16:41:56: 20000000 INFO @ Sat, 24 Aug 2019 16:42:01: 23000000 INFO @ Sat, 24 Aug 2019 16:42:02: 13000000 INFO @ Sat, 24 Aug 2019 16:42:03: 21000000 INFO @ Sat, 24 Aug 2019 16:42:08: 24000000 INFO @ Sat, 24 Aug 2019 16:42:10: 22000000 INFO @ Sat, 24 Aug 2019 16:42:11: 14000000 INFO @ Sat, 24 Aug 2019 16:42:16: 25000000 INFO @ Sat, 24 Aug 2019 16:42:17: 23000000 INFO @ Sat, 24 Aug 2019 16:42:20: 15000000 INFO @ Sat, 24 Aug 2019 16:42:21: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:42:21: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:42:21: #1 total tags in treatment: 25641442 INFO @ Sat, 24 Aug 2019 16:42:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:42:21: #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 16:42:22: #1 tags after filtering in treatment: 25641345 INFO @ Sat, 24 Aug 2019 16:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:42:22: #1 finished! INFO @ Sat, 24 Aug 2019 16:42:22: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:42:24: 24000000 INFO @ Sat, 24 Aug 2019 16:42:25: #2 number of paired peaks: 6846 INFO @ Sat, 24 Aug 2019 16:42:25: start model_add_line... INFO @ Sat, 24 Aug 2019 16:42:25: start X-correlation... INFO @ Sat, 24 Aug 2019 16:42:25: end of X-cor INFO @ Sat, 24 Aug 2019 16:42:25: #2 finished! INFO @ Sat, 24 Aug 2019 16:42:25: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 16:42:25: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 24 Aug 2019 16:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.05_model.r WARNING @ Sat, 24 Aug 2019 16:42:25: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:42:25: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 24 Aug 2019 16:42:25: #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 16:42:25: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:42:28: 16000000 INFO @ Sat, 24 Aug 2019 16:42:31: 25000000 INFO @ Sat, 24 Aug 2019 16:42:36: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:42:36: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:42:36: #1 total tags in treatment: 25641442 INFO @ Sat, 24 Aug 2019 16:42:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:42:36: #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 16:42:37: #1 tags after filtering in treatment: 25641345 INFO @ Sat, 24 Aug 2019 16:42:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:42:37: #1 finished! INFO @ Sat, 24 Aug 2019 16:42:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:42:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:42:37: 17000000 INFO @ Sat, 24 Aug 2019 16:42:40: #2 number of paired peaks: 6846 INFO @ Sat, 24 Aug 2019 16:42:40: start model_add_line... INFO @ Sat, 24 Aug 2019 16:42:40: start X-correlation... INFO @ Sat, 24 Aug 2019 16:42:40: end of X-cor INFO @ Sat, 24 Aug 2019 16:42:40: #2 finished! INFO @ Sat, 24 Aug 2019 16:42:40: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 16:42:40: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 24 Aug 2019 16:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.10_model.r WARNING @ Sat, 24 Aug 2019 16:42:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:42:40: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 24 Aug 2019 16:42:40: #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 16:42:40: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:42:46: 18000000 INFO @ Sat, 24 Aug 2019 16:42:55: 19000000 INFO @ Sat, 24 Aug 2019 16:43:03: 20000000 INFO @ Sat, 24 Aug 2019 16:43:12: 21000000 INFO @ Sat, 24 Aug 2019 16:43:21: 22000000 INFO @ Sat, 24 Aug 2019 16:43:29: 23000000 INFO @ Sat, 24 Aug 2019 16:43:38: 24000000 INFO @ Sat, 24 Aug 2019 16:43:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:43:47: 25000000 INFO @ Sat, 24 Aug 2019 16:43:53: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:43:53: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:43:53: #1 total tags in treatment: 25641442 INFO @ Sat, 24 Aug 2019 16:43:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:43:53: #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 16:43:54: #1 tags after filtering in treatment: 25641345 INFO @ Sat, 24 Aug 2019 16:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:43:54: #1 finished! INFO @ Sat, 24 Aug 2019 16:43:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:43:57: #2 number of paired peaks: 6846 INFO @ Sat, 24 Aug 2019 16:43:57: start model_add_line... INFO @ Sat, 24 Aug 2019 16:43:57: start X-correlation... INFO @ Sat, 24 Aug 2019 16:43:57: end of X-cor INFO @ Sat, 24 Aug 2019 16:43:57: #2 finished! INFO @ Sat, 24 Aug 2019 16:43:57: #2 predicted fragment length is 42 bps INFO @ Sat, 24 Aug 2019 16:43:57: #2 alternative fragment length(s) may be 42 bps INFO @ Sat, 24 Aug 2019 16:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.20_model.r WARNING @ Sat, 24 Aug 2019 16:43:57: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:43:57: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Sat, 24 Aug 2019 16:43:57: #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 16:43:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:44:00: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.05_summits.bed INFO @ Sat, 24 Aug 2019 16:44:24: Done! pass1 - making usageList (71 chroms): 3 millis pass2 - checking and writing primary data (4435 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.10_summits.bed INFO @ Sat, 24 Aug 2019 16:44:40: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1629 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:45:17: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX023852/SRX023852.20_summits.bed INFO @ Sat, 24 Aug 2019 16:45:56: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (580 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。