Job ID = 2590176 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:52:22 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 : 13,404,715 reads read : 13,404,715 reads written : 13,404,715 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: 00:02:15 13404715 reads; of these: 13404715 (100.00%) were unpaired; of these: 4136576 (30.86%) aligned 0 times 8060642 (60.13%) aligned exactly 1 time 1207497 (9.01%) aligned >1 times 69.14% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 2665189 / 9268139 = 0.2876 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 20:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.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 20:07:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:07:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.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 20:07:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:07:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:07:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.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 20:07:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:07:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:07:26: 1000000 INFO @ Mon, 12 Aug 2019 20:07:28: 1000000 INFO @ Mon, 12 Aug 2019 20:07:31: 1000000 INFO @ Mon, 12 Aug 2019 20:07:34: 2000000 INFO @ Mon, 12 Aug 2019 20:07:35: 2000000 INFO @ Mon, 12 Aug 2019 20:07:40: 2000000 INFO @ Mon, 12 Aug 2019 20:07:42: 3000000 INFO @ Mon, 12 Aug 2019 20:07:43: 3000000 INFO @ Mon, 12 Aug 2019 20:07:49: 4000000 INFO @ Mon, 12 Aug 2019 20:07:50: 3000000 INFO @ Mon, 12 Aug 2019 20:07:50: 4000000 INFO @ Mon, 12 Aug 2019 20:07:57: 5000000 INFO @ Mon, 12 Aug 2019 20:07:58: 5000000 INFO @ Mon, 12 Aug 2019 20:07:59: 4000000 INFO @ Mon, 12 Aug 2019 20:08:04: 6000000 INFO @ Mon, 12 Aug 2019 20:08:06: 6000000 INFO @ Mon, 12 Aug 2019 20:08:09: 5000000 INFO @ Mon, 12 Aug 2019 20:08:09: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:08:09: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:08:09: #1 total tags in treatment: 6602950 INFO @ Mon, 12 Aug 2019 20:08:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:08:09: #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 20:08:09: #1 tags after filtering in treatment: 6602950 INFO @ Mon, 12 Aug 2019 20:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:08:09: #1 finished! INFO @ Mon, 12 Aug 2019 20:08:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:08:10: #2 number of paired peaks: 1115 INFO @ Mon, 12 Aug 2019 20:08:10: start model_add_line... INFO @ Mon, 12 Aug 2019 20:08:10: start X-correlation... INFO @ Mon, 12 Aug 2019 20:08:10: end of X-cor INFO @ Mon, 12 Aug 2019 20:08:10: #2 finished! INFO @ Mon, 12 Aug 2019 20:08:10: #2 predicted fragment length is 193 bps INFO @ Mon, 12 Aug 2019 20:08:10: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 12 Aug 2019 20:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.05_model.r INFO @ Mon, 12 Aug 2019 20:08:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:08:10: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:08:10: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:08:10: #1 total tags in treatment: 6602950 INFO @ Mon, 12 Aug 2019 20:08:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:08:10: #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 20:08:10: #1 tags after filtering in treatment: 6602950 INFO @ Mon, 12 Aug 2019 20:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:08:10: #1 finished! INFO @ Mon, 12 Aug 2019 20:08:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:08:11: #2 number of paired peaks: 1115 INFO @ Mon, 12 Aug 2019 20:08:11: start model_add_line... INFO @ Mon, 12 Aug 2019 20:08:11: start X-correlation... INFO @ Mon, 12 Aug 2019 20:08:11: end of X-cor INFO @ Mon, 12 Aug 2019 20:08:11: #2 finished! INFO @ Mon, 12 Aug 2019 20:08:11: #2 predicted fragment length is 193 bps INFO @ Mon, 12 Aug 2019 20:08:11: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 12 Aug 2019 20:08:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.10_model.r INFO @ Mon, 12 Aug 2019 20:08:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:08:18: 6000000 INFO @ Mon, 12 Aug 2019 20:08:24: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:08:24: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:08:24: #1 total tags in treatment: 6602950 INFO @ Mon, 12 Aug 2019 20:08:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:08:24: #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 20:08:24: #1 tags after filtering in treatment: 6602950 INFO @ Mon, 12 Aug 2019 20:08:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:08:24: #1 finished! INFO @ Mon, 12 Aug 2019 20:08:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:08:24: #2 number of paired peaks: 1115 INFO @ Mon, 12 Aug 2019 20:08:24: start model_add_line... INFO @ Mon, 12 Aug 2019 20:08:25: start X-correlation... INFO @ Mon, 12 Aug 2019 20:08:25: end of X-cor INFO @ Mon, 12 Aug 2019 20:08:25: #2 finished! INFO @ Mon, 12 Aug 2019 20:08:25: #2 predicted fragment length is 193 bps INFO @ Mon, 12 Aug 2019 20:08:25: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 12 Aug 2019 20:08:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.20_model.r INFO @ Mon, 12 Aug 2019 20:08:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:08:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:08:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.05_summits.bed INFO @ Mon, 12 Aug 2019 20:08:42: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4302 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:08:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:08:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.10_summits.bed INFO @ Mon, 12 Aug 2019 20:08:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2405 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:08:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495064/SRX495064.20_summits.bed INFO @ Mon, 12 Aug 2019 20:08:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1186 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。