Job ID = 1292500 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:08:49 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 : 5,595,479 reads read : 5,595,479 reads written : 5,595,479 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:01:48 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127691 (2.28%) aligned 0 times 4499805 (80.42%) aligned exactly 1 time 967983 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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_rmdupse_core] 319358 / 5467788 = 0.0584 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 @ Sun, 02 Jun 2019 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.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 @ Sun, 02 Jun 2019 19:13:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:13:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.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 @ Sun, 02 Jun 2019 19:13:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:13:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.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 @ Sun, 02 Jun 2019 19:13:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:13:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:13:53: 1000000 INFO @ Sun, 02 Jun 2019 19:13:53: 1000000 INFO @ Sun, 02 Jun 2019 19:13:54: 1000000 INFO @ Sun, 02 Jun 2019 19:14:00: 2000000 INFO @ Sun, 02 Jun 2019 19:14:02: 2000000 INFO @ Sun, 02 Jun 2019 19:14:04: 2000000 INFO @ Sun, 02 Jun 2019 19:14:08: 3000000 INFO @ Sun, 02 Jun 2019 19:14:10: 3000000 INFO @ Sun, 02 Jun 2019 19:14:14: 3000000 INFO @ Sun, 02 Jun 2019 19:14:16: 4000000 INFO @ Sun, 02 Jun 2019 19:14:19: 4000000 INFO @ Sun, 02 Jun 2019 19:14:23: 4000000 INFO @ Sun, 02 Jun 2019 19:14:24: 5000000 INFO @ Sun, 02 Jun 2019 19:14:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:14:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:14:25: #1 total tags in treatment: 5148430 INFO @ Sun, 02 Jun 2019 19:14:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:14:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:14:25: #1 tags after filtering in treatment: 5148430 INFO @ Sun, 02 Jun 2019 19:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:14:25: #1 finished! INFO @ Sun, 02 Jun 2019 19:14:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:14:25: #2 number of paired peaks: 417 WARNING @ Sun, 02 Jun 2019 19:14:25: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Sun, 02 Jun 2019 19:14:25: start model_add_line... INFO @ Sun, 02 Jun 2019 19:14:26: start X-correlation... INFO @ Sun, 02 Jun 2019 19:14:26: end of X-cor INFO @ Sun, 02 Jun 2019 19:14:26: #2 finished! INFO @ Sun, 02 Jun 2019 19:14:26: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 19:14:26: #2 alternative fragment length(s) may be 4,49,591 bps INFO @ Sun, 02 Jun 2019 19:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.10_model.r WARNING @ Sun, 02 Jun 2019 19:14:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:14:26: #2 You may need to consider one of the other alternative d(s): 4,49,591 WARNING @ Sun, 02 Jun 2019 19:14:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:14:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:14:27: 5000000 INFO @ Sun, 02 Jun 2019 19:14:28: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:14:28: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:14:28: #1 total tags in treatment: 5148430 INFO @ Sun, 02 Jun 2019 19:14:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:14:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:14:28: #1 tags after filtering in treatment: 5148430 INFO @ Sun, 02 Jun 2019 19:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:14:28: #1 finished! INFO @ Sun, 02 Jun 2019 19:14:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:14:29: #2 number of paired peaks: 417 WARNING @ Sun, 02 Jun 2019 19:14:29: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Sun, 02 Jun 2019 19:14:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:14:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:14:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:14:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:14:29: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 19:14:29: #2 alternative fragment length(s) may be 4,49,591 bps INFO @ Sun, 02 Jun 2019 19:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.20_model.r WARNING @ Sun, 02 Jun 2019 19:14:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:14:29: #2 You may need to consider one of the other alternative d(s): 4,49,591 WARNING @ Sun, 02 Jun 2019 19:14:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:14:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:14:32: 5000000 INFO @ Sun, 02 Jun 2019 19:14:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:14:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:14:33: #1 total tags in treatment: 5148430 INFO @ Sun, 02 Jun 2019 19:14:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:14:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:14:34: #1 tags after filtering in treatment: 5148430 INFO @ Sun, 02 Jun 2019 19:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:14:34: #1 finished! INFO @ Sun, 02 Jun 2019 19:14:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:14:34: #2 number of paired peaks: 417 WARNING @ Sun, 02 Jun 2019 19:14:34: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Sun, 02 Jun 2019 19:14:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:14:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:14:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:14:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:14:34: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 19:14:34: #2 alternative fragment length(s) may be 4,49,591 bps INFO @ Sun, 02 Jun 2019 19:14:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.05_model.r WARNING @ Sun, 02 Jun 2019 19:14:34: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:14:34: #2 You may need to consider one of the other alternative d(s): 4,49,591 WARNING @ Sun, 02 Jun 2019 19:14:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:14:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:14:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:14:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:14:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:14:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.10_summits.bed INFO @ Sun, 02 Jun 2019 19:14:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:14:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.20_summits.bed INFO @ Sun, 02 Jun 2019 19:14:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (141 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:14:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:14:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:14:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466476/SRX466476.05_summits.bed INFO @ Sun, 02 Jun 2019 19:14:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (559 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。