Job ID = 2640428 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) 2019-08-24T07:41:51 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 ) 2019-08-24T07:44:11 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 ) 2019-08-24T07:45:24 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 ) 2019-08-24T07:46:46 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 : 153,530,180 reads read : 153,530,180 reads written : 153,530,180 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR980345.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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 03:50:21 153530180 reads; of these: 153530180 (100.00%) were unpaired; of these: 28575429 (18.61%) aligned 0 times 94758800 (61.72%) aligned exactly 1 time 30195951 (19.67%) aligned >1 times 81.39% overall alignment rate Time searching: 03:50:26 Overall time: 03:50:26 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 52 files... [bam_rmdupse_core] 105824224 / 124954751 = 0.8469 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:08:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.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 21:08:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:08:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:29: 1000000 INFO @ Sat, 24 Aug 2019 21:08:39: 2000000 INFO @ Sat, 24 Aug 2019 21:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.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 21:08:49: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:08:49: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:08:49: 3000000 INFO @ Sat, 24 Aug 2019 21:08:57: 1000000 INFO @ Sat, 24 Aug 2019 21:09:00: 4000000 INFO @ Sat, 24 Aug 2019 21:09:05: 2000000 INFO @ Sat, 24 Aug 2019 21:09:10: 5000000 INFO @ Sat, 24 Aug 2019 21:09:12: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.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 21:09:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:09:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:09:20: 4000000 INFO @ Sat, 24 Aug 2019 21:09:21: 6000000 INFO @ Sat, 24 Aug 2019 21:09:28: 5000000 INFO @ Sat, 24 Aug 2019 21:09:30: 1000000 INFO @ Sat, 24 Aug 2019 21:09:32: 7000000 INFO @ Sat, 24 Aug 2019 21:09:36: 6000000 INFO @ Sat, 24 Aug 2019 21:09:42: 2000000 INFO @ Sat, 24 Aug 2019 21:09:43: 8000000 INFO @ Sat, 24 Aug 2019 21:09:44: 7000000 INFO @ Sat, 24 Aug 2019 21:09:52: 8000000 INFO @ Sat, 24 Aug 2019 21:09:53: 3000000 INFO @ Sat, 24 Aug 2019 21:09:54: 9000000 INFO @ Sat, 24 Aug 2019 21:10:00: 9000000 INFO @ Sat, 24 Aug 2019 21:10:04: 4000000 INFO @ Sat, 24 Aug 2019 21:10:06: 10000000 INFO @ Sat, 24 Aug 2019 21:10:08: 10000000 INFO @ Sat, 24 Aug 2019 21:10:15: 11000000 INFO @ Sat, 24 Aug 2019 21:10:16: 5000000 INFO @ Sat, 24 Aug 2019 21:10:17: 11000000 INFO @ Sat, 24 Aug 2019 21:10:23: 12000000 INFO @ Sat, 24 Aug 2019 21:10:27: 6000000 INFO @ Sat, 24 Aug 2019 21:10:28: 12000000 INFO @ Sat, 24 Aug 2019 21:10:31: 13000000 INFO @ Sat, 24 Aug 2019 21:10:38: 7000000 INFO @ Sat, 24 Aug 2019 21:10:39: 14000000 INFO @ Sat, 24 Aug 2019 21:10:40: 13000000 INFO @ Sat, 24 Aug 2019 21:10:47: 15000000 INFO @ Sat, 24 Aug 2019 21:10:49: 8000000 INFO @ Sat, 24 Aug 2019 21:10:51: 14000000 INFO @ Sat, 24 Aug 2019 21:10:55: 16000000 INFO @ Sat, 24 Aug 2019 21:11:01: 9000000 INFO @ Sat, 24 Aug 2019 21:11:03: 15000000 INFO @ Sat, 24 Aug 2019 21:11:03: 17000000 INFO @ Sat, 24 Aug 2019 21:11:11: 18000000 INFO @ Sat, 24 Aug 2019 21:11:13: 10000000 INFO @ Sat, 24 Aug 2019 21:11:14: 16000000 INFO @ Sat, 24 Aug 2019 21:11:21: 19000000 INFO @ Sat, 24 Aug 2019 21:11:22: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:11:22: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:11:22: #1 total tags in treatment: 19130527 INFO @ Sat, 24 Aug 2019 21:11:22: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:22: #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 21:11:23: #1 tags after filtering in treatment: 19130426 INFO @ Sat, 24 Aug 2019 21:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:11:23: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:23: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:27: 11000000 INFO @ Sat, 24 Aug 2019 21:11:27: 17000000 INFO @ Sat, 24 Aug 2019 21:11:28: #2 number of paired peaks: 50082 INFO @ Sat, 24 Aug 2019 21:11:28: start model_add_line... INFO @ Sat, 24 Aug 2019 21:11:29: start X-correlation... INFO @ Sat, 24 Aug 2019 21:11:29: end of X-cor INFO @ Sat, 24 Aug 2019 21:11:29: #2 finished! INFO @ Sat, 24 Aug 2019 21:11:29: #2 predicted fragment length is 53 bps INFO @ Sat, 24 Aug 2019 21:11:29: #2 alternative fragment length(s) may be 53,290,472,517 bps INFO @ Sat, 24 Aug 2019 21:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.10_model.r WARNING @ Sat, 24 Aug 2019 21:11:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:11:29: #2 You may need to consider one of the other alternative d(s): 53,290,472,517 WARNING @ Sat, 24 Aug 2019 21:11:29: #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 21:11:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:11:38: 12000000 INFO @ Sat, 24 Aug 2019 21:11:39: 18000000 INFO @ Sat, 24 Aug 2019 21:11:50: 13000000 INFO @ Sat, 24 Aug 2019 21:11:51: 19000000 INFO @ Sat, 24 Aug 2019 21:11:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:11:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:11:53: #1 total tags in treatment: 19130527 INFO @ Sat, 24 Aug 2019 21:11:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:11:53: #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 21:11:53: #1 tags after filtering in treatment: 19130426 INFO @ Sat, 24 Aug 2019 21:11:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:11:53: #1 finished! INFO @ Sat, 24 Aug 2019 21:11:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:11:58: #2 number of paired peaks: 50082 INFO @ Sat, 24 Aug 2019 21:11:58: start model_add_line... INFO @ Sat, 24 Aug 2019 21:11:58: start X-correlation... INFO @ Sat, 24 Aug 2019 21:11:58: end of X-cor INFO @ Sat, 24 Aug 2019 21:11:58: #2 finished! INFO @ Sat, 24 Aug 2019 21:11:58: #2 predicted fragment length is 53 bps INFO @ Sat, 24 Aug 2019 21:11:58: #2 alternative fragment length(s) may be 53,290,472,517 bps INFO @ Sat, 24 Aug 2019 21:11:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.05_model.r WARNING @ Sat, 24 Aug 2019 21:11:58: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:11:58: #2 You may need to consider one of the other alternative d(s): 53,290,472,517 WARNING @ Sat, 24 Aug 2019 21:11:58: #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 21:11:58: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:11:59: 14000000 INFO @ Sat, 24 Aug 2019 21:12:07: 15000000 INFO @ Sat, 24 Aug 2019 21:12:15: 16000000 INFO @ Sat, 24 Aug 2019 21:12:23: 17000000 INFO @ Sat, 24 Aug 2019 21:12:31: 18000000 INFO @ Sat, 24 Aug 2019 21:12:33: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:12:39: 19000000 INFO @ Sat, 24 Aug 2019 21:12:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 21:12:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 21:12:40: #1 total tags in treatment: 19130527 INFO @ Sat, 24 Aug 2019 21:12:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:12:40: #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 21:12:41: #1 tags after filtering in treatment: 19130426 INFO @ Sat, 24 Aug 2019 21:12:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:12:41: #1 finished! INFO @ Sat, 24 Aug 2019 21:12:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:12:45: #2 number of paired peaks: 50082 INFO @ Sat, 24 Aug 2019 21:12:45: start model_add_line... INFO @ Sat, 24 Aug 2019 21:12:45: start X-correlation... INFO @ Sat, 24 Aug 2019 21:12:45: end of X-cor INFO @ Sat, 24 Aug 2019 21:12:45: #2 finished! INFO @ Sat, 24 Aug 2019 21:12:45: #2 predicted fragment length is 53 bps INFO @ Sat, 24 Aug 2019 21:12:45: #2 alternative fragment length(s) may be 53,290,472,517 bps INFO @ Sat, 24 Aug 2019 21:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.20_model.r WARNING @ Sat, 24 Aug 2019 21:12:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:12:45: #2 You may need to consider one of the other alternative d(s): 53,290,472,517 WARNING @ Sat, 24 Aug 2019 21:12:45: #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 21:12:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:12:58: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.10_summits.bed INFO @ Sat, 24 Aug 2019 21:13:05: Done! pass1 - making usageList (161 chroms): 9 millis pass2 - checking and writing primary data (28134 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.05_summits.bed INFO @ Sat, 24 Aug 2019 21:13:31: Done! pass1 - making usageList (265 chroms): 19 millis pass2 - checking and writing primary data (78156 records, 4 fields): 105 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:13:45: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:14:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:14:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX349433/SRX349433.20_summits.bed INFO @ Sat, 24 Aug 2019 21:14:15: Done! pass1 - making usageList (76 chroms): 4 millis pass2 - checking and writing primary data (5341 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。