Job ID = 2589928 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:31 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 ) 2019-08-12T09:52:07 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 ) 2019-08-12T09:52:14 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 : 22,299,748 reads read : 22,299,748 reads written : 22,299,748 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: 00:05:52 22299748 reads; of these: 22299748 (100.00%) were unpaired; of these: 905106 (4.06%) aligned 0 times 18192522 (81.58%) aligned exactly 1 time 3202120 (14.36%) aligned >1 times 95.94% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4862183 / 21394642 = 0.2273 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 19:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.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 19:10:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.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 19:10:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.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 19:10:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:10:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:10:26: 1000000 INFO @ Mon, 12 Aug 2019 19:10:27: 1000000 INFO @ Mon, 12 Aug 2019 19:10:27: 1000000 INFO @ Mon, 12 Aug 2019 19:10:34: 2000000 INFO @ Mon, 12 Aug 2019 19:10:34: 2000000 INFO @ Mon, 12 Aug 2019 19:10:34: 2000000 INFO @ Mon, 12 Aug 2019 19:10:40: 3000000 INFO @ Mon, 12 Aug 2019 19:10:41: 3000000 INFO @ Mon, 12 Aug 2019 19:10:41: 3000000 INFO @ Mon, 12 Aug 2019 19:10:47: 4000000 INFO @ Mon, 12 Aug 2019 19:10:48: 4000000 INFO @ Mon, 12 Aug 2019 19:10:48: 4000000 INFO @ Mon, 12 Aug 2019 19:10:53: 5000000 INFO @ Mon, 12 Aug 2019 19:10:55: 5000000 INFO @ Mon, 12 Aug 2019 19:10:56: 5000000 INFO @ Mon, 12 Aug 2019 19:11:00: 6000000 INFO @ Mon, 12 Aug 2019 19:11:02: 6000000 INFO @ Mon, 12 Aug 2019 19:11:03: 6000000 INFO @ Mon, 12 Aug 2019 19:11:08: 7000000 INFO @ Mon, 12 Aug 2019 19:11:10: 7000000 INFO @ Mon, 12 Aug 2019 19:11:10: 7000000 INFO @ Mon, 12 Aug 2019 19:11:15: 8000000 INFO @ Mon, 12 Aug 2019 19:11:17: 8000000 INFO @ Mon, 12 Aug 2019 19:11:17: 8000000 INFO @ Mon, 12 Aug 2019 19:11:21: 9000000 INFO @ Mon, 12 Aug 2019 19:11:24: 9000000 INFO @ Mon, 12 Aug 2019 19:11:25: 9000000 INFO @ Mon, 12 Aug 2019 19:11:29: 10000000 INFO @ Mon, 12 Aug 2019 19:11:33: 10000000 INFO @ Mon, 12 Aug 2019 19:11:33: 10000000 INFO @ Mon, 12 Aug 2019 19:11:37: 11000000 INFO @ Mon, 12 Aug 2019 19:11:39: 11000000 INFO @ Mon, 12 Aug 2019 19:11:41: 11000000 INFO @ Mon, 12 Aug 2019 19:11:44: 12000000 INFO @ Mon, 12 Aug 2019 19:11:46: 12000000 INFO @ Mon, 12 Aug 2019 19:11:48: 12000000 INFO @ Mon, 12 Aug 2019 19:11:52: 13000000 INFO @ Mon, 12 Aug 2019 19:11:52: 13000000 INFO @ Mon, 12 Aug 2019 19:11:56: 13000000 INFO @ Mon, 12 Aug 2019 19:11:59: 14000000 INFO @ Mon, 12 Aug 2019 19:11:59: 14000000 INFO @ Mon, 12 Aug 2019 19:12:04: 14000000 INFO @ Mon, 12 Aug 2019 19:12:05: 15000000 INFO @ Mon, 12 Aug 2019 19:12:07: 15000000 INFO @ Mon, 12 Aug 2019 19:12:11: 16000000 INFO @ Mon, 12 Aug 2019 19:12:12: 15000000 INFO @ Mon, 12 Aug 2019 19:12:14: 16000000 INFO @ Mon, 12 Aug 2019 19:12:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:12:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:12:15: #1 total tags in treatment: 16532459 INFO @ Mon, 12 Aug 2019 19:12:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:12:15: #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 19:12:16: #1 tags after filtering in treatment: 16532459 INFO @ Mon, 12 Aug 2019 19:12:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:12:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:12:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:12:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:12:17: #2 number of paired peaks: 483 WARNING @ Mon, 12 Aug 2019 19:12:17: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Mon, 12 Aug 2019 19:12:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:12:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:12:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:12:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:12:17: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 19:12:17: #2 alternative fragment length(s) may be 3,130,148 bps INFO @ Mon, 12 Aug 2019 19:12:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.05_model.r INFO @ Mon, 12 Aug 2019 19:12:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:12:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:12:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:12:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:12:18: #1 total tags in treatment: 16532459 INFO @ Mon, 12 Aug 2019 19:12:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:12:18: #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 19:12:19: #1 tags after filtering in treatment: 16532459 INFO @ Mon, 12 Aug 2019 19:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:12:19: #1 finished! INFO @ Mon, 12 Aug 2019 19:12:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:12:20: 16000000 INFO @ Mon, 12 Aug 2019 19:12:20: #2 number of paired peaks: 483 WARNING @ Mon, 12 Aug 2019 19:12:20: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Mon, 12 Aug 2019 19:12:20: start model_add_line... INFO @ Mon, 12 Aug 2019 19:12:20: start X-correlation... INFO @ Mon, 12 Aug 2019 19:12:20: end of X-cor INFO @ Mon, 12 Aug 2019 19:12:20: #2 finished! INFO @ Mon, 12 Aug 2019 19:12:20: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 19:12:20: #2 alternative fragment length(s) may be 3,130,148 bps INFO @ Mon, 12 Aug 2019 19:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.20_model.r INFO @ Mon, 12 Aug 2019 19:12:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:12:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:12:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:12:24: #1 total tags in treatment: 16532459 INFO @ Mon, 12 Aug 2019 19:12:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:12:24: #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 19:12:24: #1 tags after filtering in treatment: 16532459 INFO @ Mon, 12 Aug 2019 19:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:12:24: #1 finished! INFO @ Mon, 12 Aug 2019 19:12:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:12:26: #2 number of paired peaks: 483 WARNING @ Mon, 12 Aug 2019 19:12:26: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Mon, 12 Aug 2019 19:12:26: start model_add_line... INFO @ Mon, 12 Aug 2019 19:12:26: start X-correlation... INFO @ Mon, 12 Aug 2019 19:12:26: end of X-cor INFO @ Mon, 12 Aug 2019 19:12:26: #2 finished! INFO @ Mon, 12 Aug 2019 19:12:26: #2 predicted fragment length is 148 bps INFO @ Mon, 12 Aug 2019 19:12:26: #2 alternative fragment length(s) may be 3,130,148 bps INFO @ Mon, 12 Aug 2019 19:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.10_model.r INFO @ Mon, 12 Aug 2019 19:12:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:13:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:13:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:13:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.05_summits.bed INFO @ Mon, 12 Aug 2019 19:13:22: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (10215 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.20_summits.bed INFO @ Mon, 12 Aug 2019 19:13:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331340/SRX331340.10_summits.bed INFO @ Mon, 12 Aug 2019 19:13:31: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4036 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。