Job ID = 1291666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:12:33 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 ) 2019-06-02T07:12:33 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 : 54,569,107 reads read : 54,569,107 reads written : 54,569,107 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: 00:12:19 54569107 reads; of these: 54569107 (100.00%) were unpaired; of these: 3422642 (6.27%) aligned 0 times 43668217 (80.02%) aligned exactly 1 time 7478248 (13.70%) aligned >1 times 93.73% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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 24 files... [bam_rmdupse_core] 23957165 / 51146465 = 0.4684 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 16:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.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 16:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.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 16:42:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:42:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:42:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:42:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.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 16:42:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:42:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:42:19: 1000000 INFO @ Sun, 02 Jun 2019 16:42:19: 1000000 INFO @ Sun, 02 Jun 2019 16:42:19: 1000000 INFO @ Sun, 02 Jun 2019 16:42:27: 2000000 INFO @ Sun, 02 Jun 2019 16:42:27: 2000000 INFO @ Sun, 02 Jun 2019 16:42:28: 2000000 INFO @ Sun, 02 Jun 2019 16:42:36: 3000000 INFO @ Sun, 02 Jun 2019 16:42:36: 3000000 INFO @ Sun, 02 Jun 2019 16:42:37: 3000000 INFO @ Sun, 02 Jun 2019 16:42:45: 4000000 INFO @ Sun, 02 Jun 2019 16:42:45: 4000000 INFO @ Sun, 02 Jun 2019 16:42:46: 4000000 INFO @ Sun, 02 Jun 2019 16:42:53: 5000000 INFO @ Sun, 02 Jun 2019 16:42:54: 5000000 INFO @ Sun, 02 Jun 2019 16:42:55: 5000000 INFO @ Sun, 02 Jun 2019 16:43:00: 6000000 INFO @ Sun, 02 Jun 2019 16:43:01: 6000000 INFO @ Sun, 02 Jun 2019 16:43:03: 6000000 INFO @ Sun, 02 Jun 2019 16:43:08: 7000000 INFO @ Sun, 02 Jun 2019 16:43:09: 7000000 INFO @ Sun, 02 Jun 2019 16:43:12: 7000000 INFO @ Sun, 02 Jun 2019 16:43:15: 8000000 INFO @ Sun, 02 Jun 2019 16:43:16: 8000000 INFO @ Sun, 02 Jun 2019 16:43:21: 8000000 INFO @ Sun, 02 Jun 2019 16:43:23: 9000000 INFO @ Sun, 02 Jun 2019 16:43:23: 9000000 INFO @ Sun, 02 Jun 2019 16:43:30: 9000000 INFO @ Sun, 02 Jun 2019 16:43:30: 10000000 INFO @ Sun, 02 Jun 2019 16:43:31: 10000000 INFO @ Sun, 02 Jun 2019 16:43:38: 11000000 INFO @ Sun, 02 Jun 2019 16:43:38: 10000000 INFO @ Sun, 02 Jun 2019 16:43:38: 11000000 INFO @ Sun, 02 Jun 2019 16:43:45: 12000000 INFO @ Sun, 02 Jun 2019 16:43:46: 12000000 INFO @ Sun, 02 Jun 2019 16:43:47: 11000000 INFO @ Sun, 02 Jun 2019 16:43:53: 13000000 INFO @ Sun, 02 Jun 2019 16:43:53: 13000000 INFO @ Sun, 02 Jun 2019 16:43:56: 12000000 INFO @ Sun, 02 Jun 2019 16:44:00: 14000000 INFO @ Sun, 02 Jun 2019 16:44:01: 14000000 INFO @ Sun, 02 Jun 2019 16:44:04: 13000000 INFO @ Sun, 02 Jun 2019 16:44:08: 15000000 INFO @ Sun, 02 Jun 2019 16:44:09: 15000000 INFO @ Sun, 02 Jun 2019 16:44:13: 14000000 INFO @ Sun, 02 Jun 2019 16:44:15: 16000000 INFO @ Sun, 02 Jun 2019 16:44:16: 16000000 INFO @ Sun, 02 Jun 2019 16:44:22: 15000000 INFO @ Sun, 02 Jun 2019 16:44:22: 17000000 INFO @ Sun, 02 Jun 2019 16:44:24: 17000000 INFO @ Sun, 02 Jun 2019 16:44:30: 18000000 INFO @ Sun, 02 Jun 2019 16:44:30: 16000000 INFO @ Sun, 02 Jun 2019 16:44:31: 18000000 INFO @ Sun, 02 Jun 2019 16:44:37: 19000000 INFO @ Sun, 02 Jun 2019 16:44:38: 19000000 INFO @ Sun, 02 Jun 2019 16:44:39: 17000000 INFO @ Sun, 02 Jun 2019 16:44:44: 20000000 INFO @ Sun, 02 Jun 2019 16:44:46: 20000000 INFO @ Sun, 02 Jun 2019 16:44:47: 18000000 INFO @ Sun, 02 Jun 2019 16:44:52: 21000000 INFO @ Sun, 02 Jun 2019 16:44:53: 21000000 INFO @ Sun, 02 Jun 2019 16:44:56: 19000000 INFO @ Sun, 02 Jun 2019 16:44:59: 22000000 INFO @ Sun, 02 Jun 2019 16:45:01: 22000000 INFO @ Sun, 02 Jun 2019 16:45:04: 20000000 INFO @ Sun, 02 Jun 2019 16:45:07: 23000000 INFO @ Sun, 02 Jun 2019 16:45:08: 23000000 INFO @ Sun, 02 Jun 2019 16:45:13: 21000000 INFO @ Sun, 02 Jun 2019 16:45:14: 24000000 INFO @ Sun, 02 Jun 2019 16:45:16: 24000000 INFO @ Sun, 02 Jun 2019 16:45:21: 22000000 INFO @ Sun, 02 Jun 2019 16:45:22: 25000000 INFO @ Sun, 02 Jun 2019 16:45:23: 25000000 INFO @ Sun, 02 Jun 2019 16:45:29: 26000000 INFO @ Sun, 02 Jun 2019 16:45:29: 23000000 INFO @ Sun, 02 Jun 2019 16:45:31: 26000000 INFO @ Sun, 02 Jun 2019 16:45:37: 27000000 INFO @ Sun, 02 Jun 2019 16:45:38: 24000000 INFO @ Sun, 02 Jun 2019 16:45:38: 27000000 INFO @ Sun, 02 Jun 2019 16:45:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:45:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:45:38: #1 total tags in treatment: 27189300 INFO @ Sun, 02 Jun 2019 16:45:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:45:38: #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 16:45:39: #1 tags after filtering in treatment: 27189300 INFO @ Sun, 02 Jun 2019 16:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:45:39: #1 finished! INFO @ Sun, 02 Jun 2019 16:45:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:45:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:45:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:45:40: #1 total tags in treatment: 27189300 INFO @ Sun, 02 Jun 2019 16:45:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:45:40: #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 16:45:40: #1 tags after filtering in treatment: 27189300 INFO @ Sun, 02 Jun 2019 16:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:45:40: #1 finished! INFO @ Sun, 02 Jun 2019 16:45:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:45:41: #2 number of paired peaks: 465 WARNING @ Sun, 02 Jun 2019 16:45:41: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 02 Jun 2019 16:45:41: start model_add_line... INFO @ Sun, 02 Jun 2019 16:45:41: start X-correlation... INFO @ Sun, 02 Jun 2019 16:45:41: end of X-cor INFO @ Sun, 02 Jun 2019 16:45:41: #2 finished! INFO @ Sun, 02 Jun 2019 16:45:41: #2 predicted fragment length is 240 bps INFO @ Sun, 02 Jun 2019 16:45:41: #2 alternative fragment length(s) may be 4,240 bps INFO @ Sun, 02 Jun 2019 16:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.05_model.r INFO @ Sun, 02 Jun 2019 16:45:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:45:43: #2 number of paired peaks: 465 WARNING @ Sun, 02 Jun 2019 16:45:43: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 02 Jun 2019 16:45:43: start model_add_line... INFO @ Sun, 02 Jun 2019 16:45:43: start X-correlation... INFO @ Sun, 02 Jun 2019 16:45:43: end of X-cor INFO @ Sun, 02 Jun 2019 16:45:43: #2 finished! INFO @ Sun, 02 Jun 2019 16:45:43: #2 predicted fragment length is 240 bps INFO @ Sun, 02 Jun 2019 16:45:43: #2 alternative fragment length(s) may be 4,240 bps INFO @ Sun, 02 Jun 2019 16:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.10_model.r INFO @ Sun, 02 Jun 2019 16:45:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:45:47: 25000000 INFO @ Sun, 02 Jun 2019 16:45:55: 26000000 INFO @ Sun, 02 Jun 2019 16:46:03: 27000000 INFO @ Sun, 02 Jun 2019 16:46:05: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:46:05: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:46:05: #1 total tags in treatment: 27189300 INFO @ Sun, 02 Jun 2019 16:46:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:46:05: #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 16:46:06: #1 tags after filtering in treatment: 27189300 INFO @ Sun, 02 Jun 2019 16:46:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:46:06: #1 finished! INFO @ Sun, 02 Jun 2019 16:46:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:46:08: #2 number of paired peaks: 465 WARNING @ Sun, 02 Jun 2019 16:46:08: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 02 Jun 2019 16:46:08: start model_add_line... INFO @ Sun, 02 Jun 2019 16:46:08: start X-correlation... INFO @ Sun, 02 Jun 2019 16:46:08: end of X-cor INFO @ Sun, 02 Jun 2019 16:46:08: #2 finished! INFO @ Sun, 02 Jun 2019 16:46:08: #2 predicted fragment length is 240 bps INFO @ Sun, 02 Jun 2019 16:46:08: #2 alternative fragment length(s) may be 4,240 bps INFO @ Sun, 02 Jun 2019 16:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.20_model.r INFO @ Sun, 02 Jun 2019 16:46:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.05_summits.bed INFO @ Sun, 02 Jun 2019 16:47:32: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (8527 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.10_summits.bed INFO @ Sun, 02 Jun 2019 16:47:34: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (6367 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769994/SRX1769994.20_summits.bed INFO @ Sun, 02 Jun 2019 16:48:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4015 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。