Job ID = 2589958 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:31 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 ) 2019-08-12T09:51:45 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 ) 2019-08-12T09:51:51 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 ) 2019-08-12T09:51:51 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 ) 2019-08-12T09:52:08 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 : 34,986,228 reads read : 34,986,228 reads written : 34,986,228 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163555.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:42 34986228 reads; of these: 34986228 (100.00%) were unpaired; of these: 537462 (1.54%) aligned 0 times 30751538 (87.90%) aligned exactly 1 time 3697228 (10.57%) aligned >1 times 98.46% overall alignment rate Time searching: 00:09:42 Overall time: 00:09:42 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 17201623 / 34448766 = 0.4993 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 @ Mon, 12 Aug 2019 19:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 19:12:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:12:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 19:12:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:12:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 19:12:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:12:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:12:51: 1000000 INFO @ Mon, 12 Aug 2019 19:12:52: 1000000 INFO @ Mon, 12 Aug 2019 19:12:55: 1000000 INFO @ Mon, 12 Aug 2019 19:12:58: 2000000 INFO @ Mon, 12 Aug 2019 19:12:58: 2000000 INFO @ Mon, 12 Aug 2019 19:13:05: 3000000 INFO @ Mon, 12 Aug 2019 19:13:05: 2000000 INFO @ Mon, 12 Aug 2019 19:13:05: 3000000 INFO @ Mon, 12 Aug 2019 19:13:11: 4000000 INFO @ Mon, 12 Aug 2019 19:13:12: 4000000 INFO @ Mon, 12 Aug 2019 19:13:15: 3000000 INFO @ Mon, 12 Aug 2019 19:13:18: 5000000 INFO @ Mon, 12 Aug 2019 19:13:19: 5000000 INFO @ Mon, 12 Aug 2019 19:13:24: 4000000 INFO @ Mon, 12 Aug 2019 19:13:25: 6000000 INFO @ Mon, 12 Aug 2019 19:13:25: 6000000 INFO @ Mon, 12 Aug 2019 19:13:32: 7000000 INFO @ Mon, 12 Aug 2019 19:13:32: 7000000 INFO @ Mon, 12 Aug 2019 19:13:33: 5000000 INFO @ Mon, 12 Aug 2019 19:13:38: 8000000 INFO @ Mon, 12 Aug 2019 19:13:39: 8000000 INFO @ Mon, 12 Aug 2019 19:13:42: 6000000 INFO @ Mon, 12 Aug 2019 19:13:45: 9000000 INFO @ Mon, 12 Aug 2019 19:13:46: 9000000 INFO @ Mon, 12 Aug 2019 19:13:50: 7000000 INFO @ Mon, 12 Aug 2019 19:13:52: 10000000 INFO @ Mon, 12 Aug 2019 19:13:53: 10000000 INFO @ Mon, 12 Aug 2019 19:13:59: 8000000 INFO @ Mon, 12 Aug 2019 19:13:59: 11000000 INFO @ Mon, 12 Aug 2019 19:14:00: 11000000 INFO @ Mon, 12 Aug 2019 19:14:08: 12000000 INFO @ Mon, 12 Aug 2019 19:14:08: 12000000 INFO @ Mon, 12 Aug 2019 19:14:08: 9000000 INFO @ Mon, 12 Aug 2019 19:14:15: 13000000 INFO @ Mon, 12 Aug 2019 19:14:15: 13000000 INFO @ Mon, 12 Aug 2019 19:14:18: 10000000 INFO @ Mon, 12 Aug 2019 19:14:23: 14000000 INFO @ Mon, 12 Aug 2019 19:14:23: 14000000 INFO @ Mon, 12 Aug 2019 19:14:27: 11000000 INFO @ Mon, 12 Aug 2019 19:14:30: 15000000 INFO @ Mon, 12 Aug 2019 19:14:31: 15000000 INFO @ Mon, 12 Aug 2019 19:14:36: 12000000 INFO @ Mon, 12 Aug 2019 19:14:38: 16000000 INFO @ Mon, 12 Aug 2019 19:14:38: 16000000 INFO @ Mon, 12 Aug 2019 19:14:45: 13000000 INFO @ Mon, 12 Aug 2019 19:14:45: 17000000 INFO @ Mon, 12 Aug 2019 19:14:46: 17000000 INFO @ Mon, 12 Aug 2019 19:14:47: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:14:47: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:14:47: #1 total tags in treatment: 17247143 INFO @ Mon, 12 Aug 2019 19:14:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:14:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:14:48: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:14:48: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:14:48: #1 total tags in treatment: 17247143 INFO @ Mon, 12 Aug 2019 19:14:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:14:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:14:48: #1 tags after filtering in treatment: 17247143 INFO @ Mon, 12 Aug 2019 19:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:14:48: #1 finished! INFO @ Mon, 12 Aug 2019 19:14:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:14:48: #1 tags after filtering in treatment: 17247143 INFO @ Mon, 12 Aug 2019 19:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:14:48: #1 finished! INFO @ Mon, 12 Aug 2019 19:14:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:14:49: #2 number of paired peaks: 125 WARNING @ Mon, 12 Aug 2019 19:14:49: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 12 Aug 2019 19:14:49: start model_add_line... INFO @ Mon, 12 Aug 2019 19:14:49: #2 number of paired peaks: 125 WARNING @ Mon, 12 Aug 2019 19:14:49: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 12 Aug 2019 19:14:49: start model_add_line... INFO @ Mon, 12 Aug 2019 19:14:49: start X-correlation... INFO @ Mon, 12 Aug 2019 19:14:49: end of X-cor INFO @ Mon, 12 Aug 2019 19:14:49: #2 finished! INFO @ Mon, 12 Aug 2019 19:14:49: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 19:14:49: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 12 Aug 2019 19:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.10_model.r WARNING @ Mon, 12 Aug 2019 19:14:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:14:49: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 12 Aug 2019 19:14:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:14:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:14:50: start X-correlation... INFO @ Mon, 12 Aug 2019 19:14:50: end of X-cor INFO @ Mon, 12 Aug 2019 19:14:50: #2 finished! INFO @ Mon, 12 Aug 2019 19:14:50: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 19:14:50: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 12 Aug 2019 19:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.05_model.r WARNING @ Mon, 12 Aug 2019 19:14:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:14:50: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 12 Aug 2019 19:14:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:14:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:14:54: 14000000 INFO @ Mon, 12 Aug 2019 19:15:02: 15000000 INFO @ Mon, 12 Aug 2019 19:15:11: 16000000 INFO @ Mon, 12 Aug 2019 19:15:20: 17000000 INFO @ Mon, 12 Aug 2019 19:15:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:15:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:15:22: #1 total tags in treatment: 17247143 INFO @ Mon, 12 Aug 2019 19:15:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:15:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:15:23: #1 tags after filtering in treatment: 17247143 INFO @ Mon, 12 Aug 2019 19:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:15:23: #1 finished! INFO @ Mon, 12 Aug 2019 19:15:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:15:24: #2 number of paired peaks: 125 WARNING @ Mon, 12 Aug 2019 19:15:24: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Mon, 12 Aug 2019 19:15:24: start model_add_line... INFO @ Mon, 12 Aug 2019 19:15:24: start X-correlation... INFO @ Mon, 12 Aug 2019 19:15:24: end of X-cor INFO @ Mon, 12 Aug 2019 19:15:24: #2 finished! INFO @ Mon, 12 Aug 2019 19:15:24: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 19:15:24: #2 alternative fragment length(s) may be 2,53 bps INFO @ Mon, 12 Aug 2019 19:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.20_model.r WARNING @ Mon, 12 Aug 2019 19:15:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:15:24: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Mon, 12 Aug 2019 19:15:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:15:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:15:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.05_summits.bed INFO @ Mon, 12 Aug 2019 19:15:51: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2702 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:15:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:15:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:15:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.10_summits.bed INFO @ Mon, 12 Aug 2019 19:15:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:16:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466489/SRX466489.20_summits.bed INFO @ Mon, 12 Aug 2019 19:16:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。