Job ID = 3785923 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-11-01T05:41:13 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 ) 2019-11-01T05:41:13 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 : 4,981,526 reads read : 9,963,052 reads written : 4,981,526 reads 0-length : 4,981,526 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: 00:01:06 4981526 reads; of these: 4981526 (100.00%) were unpaired; of these: 4729767 (94.95%) aligned 0 times 96438 (1.94%) aligned exactly 1 time 155321 (3.12%) aligned >1 times 5.05% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 87268 / 251759 = 0.3466 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 01 Nov 2019 14:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 01 Nov 2019 14:44:59: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:44:59: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:45:01: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:45:01: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:45:01: #1 total tags in treatment: 164491 INFO @ Fri, 01 Nov 2019 14:45:01: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:45:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:45:01: #1 tags after filtering in treatment: 164491 INFO @ Fri, 01 Nov 2019 14:45:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:45:01: #1 finished! INFO @ Fri, 01 Nov 2019 14:45:01: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:45:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:45:01: #2 number of paired peaks: 3036 INFO @ Fri, 01 Nov 2019 14:45:01: start model_add_line... INFO @ Fri, 01 Nov 2019 14:45:01: start X-correlation... INFO @ Fri, 01 Nov 2019 14:45:01: end of X-cor INFO @ Fri, 01 Nov 2019 14:45:01: #2 finished! INFO @ Fri, 01 Nov 2019 14:45:01: #2 predicted fragment length is 77 bps INFO @ Fri, 01 Nov 2019 14:45:01: #2 alternative fragment length(s) may be 77,190,222 bps INFO @ Fri, 01 Nov 2019 14:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.05_model.r WARNING @ Fri, 01 Nov 2019 14:45:01: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:45:01: #2 You may need to consider one of the other alternative d(s): 77,190,222 WARNING @ Fri, 01 Nov 2019 14:45:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:45:01: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:45:02: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.05_peaks.xls INFO @ Fri, 01 Nov 2019 14:45:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.05_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:45:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.05_summits.bed INFO @ Fri, 01 Nov 2019 14:45:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 01 Nov 2019 14:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 01 Nov 2019 14:45:28: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:45:28: #1 read treatment tags... INFO @ Fri, 01 Nov 2019 14:45:29: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:45:29: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:45:29: #1 total tags in treatment: 164491 INFO @ Fri, 01 Nov 2019 14:45:29: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:45:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:45:29: #1 tags after filtering in treatment: 164491 INFO @ Fri, 01 Nov 2019 14:45:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:45:29: #1 finished! INFO @ Fri, 01 Nov 2019 14:45:29: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:45:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:45:30: #2 number of paired peaks: 3036 INFO @ Fri, 01 Nov 2019 14:45:30: start model_add_line... INFO @ Fri, 01 Nov 2019 14:45:30: start X-correlation... INFO @ Fri, 01 Nov 2019 14:45:30: end of X-cor INFO @ Fri, 01 Nov 2019 14:45:30: #2 finished! INFO @ Fri, 01 Nov 2019 14:45:30: #2 predicted fragment length is 77 bps INFO @ Fri, 01 Nov 2019 14:45:30: #2 alternative fragment length(s) may be 77,190,222 bps INFO @ Fri, 01 Nov 2019 14:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.10_model.r WARNING @ Fri, 01 Nov 2019 14:45:30: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:45:30: #2 You may need to consider one of the other alternative d(s): 77,190,222 WARNING @ Fri, 01 Nov 2019 14:45:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:45:30: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:45:30: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.10_peaks.xls INFO @ Fri, 01 Nov 2019 14:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.10_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.10_summits.bed INFO @ Fri, 01 Nov 2019 14:45:30: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Fri, 01 Nov 2019 14:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 01 Nov 2019 14:45:58: #1 read tag files... INFO @ Fri, 01 Nov 2019 14:45:58: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 01 Nov 2019 14:45:59: #1 tag size is determined as 76 bps INFO @ Fri, 01 Nov 2019 14:45:59: #1 tag size = 76 INFO @ Fri, 01 Nov 2019 14:45:59: #1 total tags in treatment: 164491 INFO @ Fri, 01 Nov 2019 14:45:59: #1 user defined the maximum tags... INFO @ Fri, 01 Nov 2019 14:45:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 01 Nov 2019 14:45:59: #1 tags after filtering in treatment: 164491 INFO @ Fri, 01 Nov 2019 14:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 01 Nov 2019 14:45:59: #1 finished! INFO @ Fri, 01 Nov 2019 14:45:59: #2 Build Peak Model... INFO @ Fri, 01 Nov 2019 14:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 01 Nov 2019 14:45:59: #2 number of paired peaks: 3036 INFO @ Fri, 01 Nov 2019 14:45:59: start model_add_line... INFO @ Fri, 01 Nov 2019 14:45:59: start X-correlation... INFO @ Fri, 01 Nov 2019 14:46:00: end of X-cor INFO @ Fri, 01 Nov 2019 14:46:00: #2 finished! INFO @ Fri, 01 Nov 2019 14:46:00: #2 predicted fragment length is 77 bps INFO @ Fri, 01 Nov 2019 14:46:00: #2 alternative fragment length(s) may be 77,190,222 bps INFO @ Fri, 01 Nov 2019 14:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.20_model.r WARNING @ Fri, 01 Nov 2019 14:46:00: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 01 Nov 2019 14:46:00: #2 You may need to consider one of the other alternative d(s): 77,190,222 WARNING @ Fri, 01 Nov 2019 14:46:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 01 Nov 2019 14:46:00: #3 Call peaks... INFO @ Fri, 01 Nov 2019 14:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 01 Nov 2019 14:46:00: #3 Call peaks for each chromosome... INFO @ Fri, 01 Nov 2019 14:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.20_peaks.xls INFO @ Fri, 01 Nov 2019 14:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.20_peaks.narrowPeak INFO @ Fri, 01 Nov 2019 14:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6370203/SRX6370203.20_summits.bed INFO @ Fri, 01 Nov 2019 14:46:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis CompletedMACS2peakCalling