Job ID = 2589957 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:51 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 ) spots read : 8,667,423 reads read : 8,667,423 reads written : 8,667,423 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:12 8667423 reads; of these: 8667423 (100.00%) were unpaired; of these: 153221 (1.77%) aligned 0 times 7020872 (81.00%) aligned exactly 1 time 1493330 (17.23%) aligned >1 times 98.23% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 809162 / 8514202 = 0.0950 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 19:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.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 19:00:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.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 19:00:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.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 19:00:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:00:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:00:12: 1000000 INFO @ Mon, 12 Aug 2019 19:00:13: 1000000 INFO @ Mon, 12 Aug 2019 19:00:14: 1000000 INFO @ Mon, 12 Aug 2019 19:00:19: 2000000 INFO @ Mon, 12 Aug 2019 19:00:20: 2000000 INFO @ Mon, 12 Aug 2019 19:00:23: 2000000 INFO @ Mon, 12 Aug 2019 19:00:27: 3000000 INFO @ Mon, 12 Aug 2019 19:00:28: 3000000 INFO @ Mon, 12 Aug 2019 19:00:32: 3000000 INFO @ Mon, 12 Aug 2019 19:00:35: 4000000 INFO @ Mon, 12 Aug 2019 19:00:36: 4000000 INFO @ Mon, 12 Aug 2019 19:00:40: 4000000 INFO @ Mon, 12 Aug 2019 19:00:43: 5000000 INFO @ Mon, 12 Aug 2019 19:00:44: 5000000 INFO @ Mon, 12 Aug 2019 19:00:49: 5000000 INFO @ Mon, 12 Aug 2019 19:00:51: 6000000 INFO @ Mon, 12 Aug 2019 19:00:52: 6000000 INFO @ Mon, 12 Aug 2019 19:00:58: 6000000 INFO @ Mon, 12 Aug 2019 19:00:59: 7000000 INFO @ Mon, 12 Aug 2019 19:01:00: 7000000 INFO @ Mon, 12 Aug 2019 19:01:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:04: #1 total tags in treatment: 7705040 INFO @ Mon, 12 Aug 2019 19:01:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:04: #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 19:01:04: #1 tags after filtering in treatment: 7705040 INFO @ Mon, 12 Aug 2019 19:01:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:04: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:05: #2 number of paired peaks: 369 WARNING @ Mon, 12 Aug 2019 19:01:05: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:05: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:05: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:05: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:05: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:05: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 19:01:05: #2 alternative fragment length(s) may be 3,49,485,516 bps INFO @ Mon, 12 Aug 2019 19:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.05_model.r WARNING @ Mon, 12 Aug 2019 19:01:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:05: #2 You may need to consider one of the other alternative d(s): 3,49,485,516 WARNING @ Mon, 12 Aug 2019 19:01:05: #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 19:01:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:05: #1 total tags in treatment: 7705040 INFO @ Mon, 12 Aug 2019 19:01:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:05: #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 19:01:05: #1 tags after filtering in treatment: 7705040 INFO @ Mon, 12 Aug 2019 19:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:05: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:06: #2 number of paired peaks: 369 WARNING @ Mon, 12 Aug 2019 19:01:06: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:06: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:06: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:06: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:06: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:06: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 19:01:06: #2 alternative fragment length(s) may be 3,49,485,516 bps INFO @ Mon, 12 Aug 2019 19:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.10_model.r WARNING @ Mon, 12 Aug 2019 19:01:06: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:06: #2 You may need to consider one of the other alternative d(s): 3,49,485,516 WARNING @ Mon, 12 Aug 2019 19:01:06: #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 19:01:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:07: 7000000 INFO @ Mon, 12 Aug 2019 19:01:13: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:01:13: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:01:13: #1 total tags in treatment: 7705040 INFO @ Mon, 12 Aug 2019 19:01:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:13: #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 19:01:13: #1 tags after filtering in treatment: 7705040 INFO @ Mon, 12 Aug 2019 19:01:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:13: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:14: #2 number of paired peaks: 369 WARNING @ Mon, 12 Aug 2019 19:01:14: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:14: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:14: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 19:01:14: #2 alternative fragment length(s) may be 3,49,485,516 bps INFO @ Mon, 12 Aug 2019 19:01:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.20_model.r WARNING @ Mon, 12 Aug 2019 19:01:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:14: #2 You may need to consider one of the other alternative d(s): 3,49,485,516 WARNING @ Mon, 12 Aug 2019 19:01:14: #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 19:01:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.05_summits.bed INFO @ Mon, 12 Aug 2019 19:01:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.10_summits.bed INFO @ Mon, 12 Aug 2019 19:01:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466488/SRX466488.20_summits.bed INFO @ Mon, 12 Aug 2019 19:01:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 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。