Job ID = 2590175 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:53:12 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 ) 2019-08-12T10:53:27 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 ) 2019-08-12T10:53:27 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 : 14,292,658 reads read : 14,292,658 reads written : 14,292,658 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: 00:03:00 14292658 reads; of these: 14292658 (100.00%) were unpaired; of these: 1202418 (8.41%) aligned 0 times 11167434 (78.13%) aligned exactly 1 time 1922806 (13.45%) aligned >1 times 91.59% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 4943397 / 13090240 = 0.3776 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 20:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.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 20:09:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:09:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.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 20:09:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:09:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.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 20:09:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:09:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:09:32: 1000000 INFO @ Mon, 12 Aug 2019 20:09:35: 1000000 INFO @ Mon, 12 Aug 2019 20:09:35: 1000000 INFO @ Mon, 12 Aug 2019 20:09:39: 2000000 INFO @ Mon, 12 Aug 2019 20:09:41: 2000000 INFO @ Mon, 12 Aug 2019 20:09:42: 2000000 INFO @ Mon, 12 Aug 2019 20:09:45: 3000000 INFO @ Mon, 12 Aug 2019 20:09:48: 3000000 INFO @ Mon, 12 Aug 2019 20:09:49: 3000000 INFO @ Mon, 12 Aug 2019 20:09:52: 4000000 INFO @ Mon, 12 Aug 2019 20:09:54: 4000000 INFO @ Mon, 12 Aug 2019 20:09:56: 4000000 INFO @ Mon, 12 Aug 2019 20:09:58: 5000000 INFO @ Mon, 12 Aug 2019 20:10:01: 5000000 INFO @ Mon, 12 Aug 2019 20:10:04: 5000000 INFO @ Mon, 12 Aug 2019 20:10:05: 6000000 INFO @ Mon, 12 Aug 2019 20:10:07: 6000000 INFO @ Mon, 12 Aug 2019 20:10:11: 6000000 INFO @ Mon, 12 Aug 2019 20:10:11: 7000000 INFO @ Mon, 12 Aug 2019 20:10:14: 7000000 INFO @ Mon, 12 Aug 2019 20:10:18: 8000000 INFO @ Mon, 12 Aug 2019 20:10:18: 7000000 INFO @ Mon, 12 Aug 2019 20:10:19: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:10:19: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:10:19: #1 total tags in treatment: 8146843 INFO @ Mon, 12 Aug 2019 20:10:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:19: #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 20:10:19: #1 tags after filtering in treatment: 8146843 INFO @ Mon, 12 Aug 2019 20:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:19: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:20: #2 number of paired peaks: 729 WARNING @ Mon, 12 Aug 2019 20:10:20: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:20: #2 predicted fragment length is 173 bps INFO @ Mon, 12 Aug 2019 20:10:20: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 12 Aug 2019 20:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.05_model.r INFO @ Mon, 12 Aug 2019 20:10:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:20: 8000000 INFO @ Mon, 12 Aug 2019 20:10:21: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:10:21: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:10:21: #1 total tags in treatment: 8146843 INFO @ Mon, 12 Aug 2019 20:10:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:21: #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 20:10:21: #1 tags after filtering in treatment: 8146843 INFO @ Mon, 12 Aug 2019 20:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:22: #2 number of paired peaks: 729 WARNING @ Mon, 12 Aug 2019 20:10:22: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:22: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:22: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:22: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:22: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:22: #2 predicted fragment length is 173 bps INFO @ Mon, 12 Aug 2019 20:10:22: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 12 Aug 2019 20:10:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.20_model.r INFO @ Mon, 12 Aug 2019 20:10:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:25: 8000000 INFO @ Mon, 12 Aug 2019 20:10:26: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 20:10:26: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 20:10:26: #1 total tags in treatment: 8146843 INFO @ Mon, 12 Aug 2019 20:10:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:26: #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 20:10:27: #1 tags after filtering in treatment: 8146843 INFO @ Mon, 12 Aug 2019 20:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:27: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:27: #2 number of paired peaks: 729 WARNING @ Mon, 12 Aug 2019 20:10:27: Fewer paired peaks (729) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 729 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:27: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:27: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:27: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:27: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:27: #2 predicted fragment length is 173 bps INFO @ Mon, 12 Aug 2019 20:10:27: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 12 Aug 2019 20:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.10_model.r INFO @ Mon, 12 Aug 2019 20:10:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.05_summits.bed INFO @ Mon, 12 Aug 2019 20:10:57: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2455 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.20_summits.bed INFO @ Mon, 12 Aug 2019 20:10:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (748 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495063/SRX495063.10_summits.bed INFO @ Mon, 12 Aug 2019 20:11:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1395 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。