Job ID = 4288808 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-10T03:09:11 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 ) 2019-12-10T03:09:11 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 ) spots read : 16,326,334 reads read : 32,652,668 reads written : 16,326,334 reads 0-length : 16,326,334 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:08:27 16326334 reads; of these: 16326334 (100.00%) were unpaired; of these: 10141290 (62.12%) aligned 0 times 4226866 (25.89%) aligned exactly 1 time 1958178 (11.99%) aligned >1 times 37.88% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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_rmdupse_core] 416606 / 6185044 = 0.0674 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.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 @ Tue, 10 Dec 2019 12:29:25: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:29:25: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:29:33: 1000000 INFO @ Tue, 10 Dec 2019 12:29:42: 2000000 INFO @ Tue, 10 Dec 2019 12:29:52: 3000000 INFO @ Tue, 10 Dec 2019 12:29:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.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 @ Tue, 10 Dec 2019 12:29:53: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:29:53: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:30:01: 4000000 INFO @ Tue, 10 Dec 2019 12:30:02: 1000000 INFO @ Tue, 10 Dec 2019 12:30:10: 5000000 INFO @ Tue, 10 Dec 2019 12:30:12: 2000000 INFO @ Tue, 10 Dec 2019 12:30:17: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:30:17: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:30:17: #1 total tags in treatment: 5768438 INFO @ Tue, 10 Dec 2019 12:30:17: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:30:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:30:17: #1 tags after filtering in treatment: 5768167 INFO @ Tue, 10 Dec 2019 12:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:30:17: #1 finished! INFO @ Tue, 10 Dec 2019 12:30:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:30:19: #2 number of paired peaks: 8075 INFO @ Tue, 10 Dec 2019 12:30:19: start model_add_line... INFO @ Tue, 10 Dec 2019 12:30:19: start X-correlation... INFO @ Tue, 10 Dec 2019 12:30:19: end of X-cor INFO @ Tue, 10 Dec 2019 12:30:19: #2 finished! INFO @ Tue, 10 Dec 2019 12:30:19: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:30:19: #2 alternative fragment length(s) may be 51,200,236 bps INFO @ Tue, 10 Dec 2019 12:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.05_model.r WARNING @ Tue, 10 Dec 2019 12:30:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:30:19: #2 You may need to consider one of the other alternative d(s): 51,200,236 WARNING @ Tue, 10 Dec 2019 12:30:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:30:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:30:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:30:22: 3000000 INFO @ Tue, 10 Dec 2019 12:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.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 @ Tue, 10 Dec 2019 12:30:23: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:30:23: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:30:31: 1000000 INFO @ Tue, 10 Dec 2019 12:30:33: 4000000 INFO @ Tue, 10 Dec 2019 12:30:38: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:30:39: 2000000 INFO @ Tue, 10 Dec 2019 12:30:43: 5000000 INFO @ Tue, 10 Dec 2019 12:30:47: 3000000 INFO @ Tue, 10 Dec 2019 12:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.05_summits.bed INFO @ Tue, 10 Dec 2019 12:30:47: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (673 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:30:51: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:30:51: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:30:51: #1 total tags in treatment: 5768438 INFO @ Tue, 10 Dec 2019 12:30:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:30:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:30:51: #1 tags after filtering in treatment: 5768167 INFO @ Tue, 10 Dec 2019 12:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:30:51: #1 finished! INFO @ Tue, 10 Dec 2019 12:30:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:30:53: #2 number of paired peaks: 8075 INFO @ Tue, 10 Dec 2019 12:30:53: start model_add_line... INFO @ Tue, 10 Dec 2019 12:30:53: start X-correlation... INFO @ Tue, 10 Dec 2019 12:30:53: end of X-cor INFO @ Tue, 10 Dec 2019 12:30:53: #2 finished! INFO @ Tue, 10 Dec 2019 12:30:53: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:30:53: #2 alternative fragment length(s) may be 51,200,236 bps INFO @ Tue, 10 Dec 2019 12:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.10_model.r WARNING @ Tue, 10 Dec 2019 12:30:53: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:30:53: #2 You may need to consider one of the other alternative d(s): 51,200,236 WARNING @ Tue, 10 Dec 2019 12:30:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:30:53: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:30:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:30:54: 4000000 INFO @ Tue, 10 Dec 2019 12:31:02: 5000000 INFO @ Tue, 10 Dec 2019 12:31:08: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:31:08: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:31:08: #1 total tags in treatment: 5768438 INFO @ Tue, 10 Dec 2019 12:31:08: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:31:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:31:08: #1 tags after filtering in treatment: 5768167 INFO @ Tue, 10 Dec 2019 12:31:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:31:08: #1 finished! INFO @ Tue, 10 Dec 2019 12:31:08: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:31:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:31:10: #2 number of paired peaks: 8075 INFO @ Tue, 10 Dec 2019 12:31:10: start model_add_line... INFO @ Tue, 10 Dec 2019 12:31:10: start X-correlation... INFO @ Tue, 10 Dec 2019 12:31:10: end of X-cor INFO @ Tue, 10 Dec 2019 12:31:10: #2 finished! INFO @ Tue, 10 Dec 2019 12:31:10: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:31:10: #2 alternative fragment length(s) may be 51,200,236 bps INFO @ Tue, 10 Dec 2019 12:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.20_model.r WARNING @ Tue, 10 Dec 2019 12:31:10: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:31:10: #2 You may need to consider one of the other alternative d(s): 51,200,236 WARNING @ Tue, 10 Dec 2019 12:31:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:31:10: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:31:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:31:12: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.10_summits.bed INFO @ Tue, 10 Dec 2019 12:31:21: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (368 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:31:29: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654066/SRX4654066.20_summits.bed INFO @ Tue, 10 Dec 2019 12:31:38: Done! pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (146 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。