Job ID = 1291880 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:58:58 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 ) 2019-06-02T07:58:58 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 ) 2019-06-02T07:58:58 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 : 33,396,816 reads read : 66,793,632 reads written : 33,396,816 reads 0-length : 33,396,816 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:46 33396816 reads; of these: 33396816 (100.00%) were unpaired; of these: 3288332 (9.85%) aligned 0 times 26193509 (78.43%) aligned exactly 1 time 3914975 (11.72%) aligned >1 times 90.15% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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 16 files... [bam_rmdupse_core] 10009211 / 30108484 = 0.3324 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 @ Sun, 02 Jun 2019 17:14:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.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 @ Sun, 02 Jun 2019 17:14:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:14:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:14:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.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 @ Sun, 02 Jun 2019 17:14:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:14:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:14:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.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 @ Sun, 02 Jun 2019 17:14:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:14:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:14:13: 1000000 INFO @ Sun, 02 Jun 2019 17:14:14: 1000000 INFO @ Sun, 02 Jun 2019 17:14:15: 1000000 INFO @ Sun, 02 Jun 2019 17:14:24: 2000000 INFO @ Sun, 02 Jun 2019 17:14:25: 2000000 INFO @ Sun, 02 Jun 2019 17:14:27: 2000000 INFO @ Sun, 02 Jun 2019 17:14:34: 3000000 INFO @ Sun, 02 Jun 2019 17:14:36: 3000000 INFO @ Sun, 02 Jun 2019 17:14:38: 3000000 INFO @ Sun, 02 Jun 2019 17:14:44: 4000000 INFO @ Sun, 02 Jun 2019 17:14:47: 4000000 INFO @ Sun, 02 Jun 2019 17:14:50: 4000000 INFO @ Sun, 02 Jun 2019 17:14:54: 5000000 INFO @ Sun, 02 Jun 2019 17:14:58: 5000000 INFO @ Sun, 02 Jun 2019 17:15:02: 5000000 INFO @ Sun, 02 Jun 2019 17:15:04: 6000000 INFO @ Sun, 02 Jun 2019 17:15:08: 6000000 INFO @ Sun, 02 Jun 2019 17:15:14: 6000000 INFO @ Sun, 02 Jun 2019 17:15:15: 7000000 INFO @ Sun, 02 Jun 2019 17:15:19: 7000000 INFO @ Sun, 02 Jun 2019 17:15:25: 8000000 INFO @ Sun, 02 Jun 2019 17:15:26: 7000000 INFO @ Sun, 02 Jun 2019 17:15:30: 8000000 INFO @ Sun, 02 Jun 2019 17:15:35: 9000000 INFO @ Sun, 02 Jun 2019 17:15:38: 8000000 INFO @ Sun, 02 Jun 2019 17:15:41: 9000000 INFO @ Sun, 02 Jun 2019 17:15:45: 10000000 INFO @ Sun, 02 Jun 2019 17:15:50: 9000000 INFO @ Sun, 02 Jun 2019 17:15:51: 10000000 INFO @ Sun, 02 Jun 2019 17:15:55: 11000000 INFO @ Sun, 02 Jun 2019 17:16:01: 10000000 INFO @ Sun, 02 Jun 2019 17:16:01: 11000000 INFO @ Sun, 02 Jun 2019 17:16:05: 12000000 INFO @ Sun, 02 Jun 2019 17:16:12: 12000000 INFO @ Sun, 02 Jun 2019 17:16:12: 11000000 INFO @ Sun, 02 Jun 2019 17:16:15: 13000000 INFO @ Sun, 02 Jun 2019 17:16:22: 13000000 INFO @ Sun, 02 Jun 2019 17:16:24: 12000000 INFO @ Sun, 02 Jun 2019 17:16:25: 14000000 INFO @ Sun, 02 Jun 2019 17:16:33: 14000000 INFO @ Sun, 02 Jun 2019 17:16:35: 15000000 INFO @ Sun, 02 Jun 2019 17:16:35: 13000000 INFO @ Sun, 02 Jun 2019 17:16:43: 15000000 INFO @ Sun, 02 Jun 2019 17:16:45: 16000000 INFO @ Sun, 02 Jun 2019 17:16:47: 14000000 INFO @ Sun, 02 Jun 2019 17:16:54: 16000000 INFO @ Sun, 02 Jun 2019 17:16:56: 17000000 INFO @ Sun, 02 Jun 2019 17:16:58: 15000000 INFO @ Sun, 02 Jun 2019 17:17:05: 17000000 INFO @ Sun, 02 Jun 2019 17:17:06: 18000000 INFO @ Sun, 02 Jun 2019 17:17:10: 16000000 INFO @ Sun, 02 Jun 2019 17:17:15: 18000000 INFO @ Sun, 02 Jun 2019 17:17:17: 19000000 INFO @ Sun, 02 Jun 2019 17:17:21: 17000000 INFO @ Sun, 02 Jun 2019 17:17:26: 19000000 INFO @ Sun, 02 Jun 2019 17:17:27: 20000000 INFO @ Sun, 02 Jun 2019 17:17:28: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:28: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:28: #1 total tags in treatment: 20099273 INFO @ Sun, 02 Jun 2019 17:17:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:17:29: #1 tags after filtering in treatment: 20099273 INFO @ Sun, 02 Jun 2019 17:17:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:29: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:31: #2 number of paired peaks: 1902 INFO @ Sun, 02 Jun 2019 17:17:31: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:31: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:31: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:31: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:31: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 17:17:31: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 02 Jun 2019 17:17:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.05_model.r INFO @ Sun, 02 Jun 2019 17:17:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:33: 18000000 INFO @ Sun, 02 Jun 2019 17:17:36: 20000000 INFO @ Sun, 02 Jun 2019 17:17:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:37: #1 total tags in treatment: 20099273 INFO @ Sun, 02 Jun 2019 17:17:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:17:38: #1 tags after filtering in treatment: 20099273 INFO @ Sun, 02 Jun 2019 17:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:38: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:40: #2 number of paired peaks: 1902 INFO @ Sun, 02 Jun 2019 17:17:40: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:40: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:40: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:40: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:40: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 17:17:40: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 02 Jun 2019 17:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.20_model.r INFO @ Sun, 02 Jun 2019 17:17:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:45: 19000000 INFO @ Sun, 02 Jun 2019 17:17:56: 20000000 INFO @ Sun, 02 Jun 2019 17:17:57: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:57: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:57: #1 total tags in treatment: 20099273 INFO @ Sun, 02 Jun 2019 17:17:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:17:57: #1 tags after filtering in treatment: 20099273 INFO @ Sun, 02 Jun 2019 17:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:57: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:59: #2 number of paired peaks: 1902 INFO @ Sun, 02 Jun 2019 17:17:59: start model_add_line... INFO @ Sun, 02 Jun 2019 17:18:00: start X-correlation... INFO @ Sun, 02 Jun 2019 17:18:00: end of X-cor INFO @ Sun, 02 Jun 2019 17:18:00: #2 finished! INFO @ Sun, 02 Jun 2019 17:18:00: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 17:18:00: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 02 Jun 2019 17:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.10_model.r INFO @ Sun, 02 Jun 2019 17:18:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:18:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:18:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.05_summits.bed INFO @ Sun, 02 Jun 2019 17:18:52: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8252 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 17:18:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:19:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.20_summits.bed INFO @ Sun, 02 Jun 2019 17:19:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2833 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737091/SRX2737091.10_summits.bed INFO @ Sun, 02 Jun 2019 17:19:21: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5466 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。