Job ID = 1293112 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T14:16:32 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 ) 2019-06-02T14:16:32 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 ) 2019-06-02T14:16:32 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 : 40,075,123 reads read : 40,075,123 reads written : 40,075,123 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: 00:15:33 40075123 reads; of these: 40075123 (100.00%) were unpaired; of these: 1276406 (3.19%) aligned 0 times 32481435 (81.05%) aligned exactly 1 time 6317282 (15.76%) aligned >1 times 96.81% overall alignment rate Time searching: 00:15:33 Overall time: 00:15:33 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] 20131272 / 38798717 = 0.5189 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 23:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.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 23:50:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:50:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.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 23:50:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:50:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.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 23:50:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:50:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:50:47: 1000000 INFO @ Sun, 02 Jun 2019 23:50:48: 1000000 INFO @ Sun, 02 Jun 2019 23:50:49: 1000000 INFO @ Sun, 02 Jun 2019 23:50:55: 2000000 INFO @ Sun, 02 Jun 2019 23:50:57: 2000000 INFO @ Sun, 02 Jun 2019 23:50:59: 2000000 INFO @ Sun, 02 Jun 2019 23:51:03: 3000000 INFO @ Sun, 02 Jun 2019 23:51:06: 3000000 INFO @ Sun, 02 Jun 2019 23:51:08: 3000000 INFO @ Sun, 02 Jun 2019 23:51:10: 4000000 INFO @ Sun, 02 Jun 2019 23:51:14: 4000000 INFO @ Sun, 02 Jun 2019 23:51:17: 4000000 INFO @ Sun, 02 Jun 2019 23:51:18: 5000000 INFO @ Sun, 02 Jun 2019 23:51:22: 5000000 INFO @ Sun, 02 Jun 2019 23:51:26: 5000000 INFO @ Sun, 02 Jun 2019 23:51:26: 6000000 INFO @ Sun, 02 Jun 2019 23:51:30: 6000000 INFO @ Sun, 02 Jun 2019 23:51:34: 7000000 INFO @ Sun, 02 Jun 2019 23:51:34: 6000000 INFO @ Sun, 02 Jun 2019 23:51:38: 7000000 INFO @ Sun, 02 Jun 2019 23:51:42: 8000000 INFO @ Sun, 02 Jun 2019 23:51:43: 7000000 INFO @ Sun, 02 Jun 2019 23:51:46: 8000000 INFO @ Sun, 02 Jun 2019 23:51:50: 9000000 INFO @ Sun, 02 Jun 2019 23:51:53: 8000000 INFO @ Sun, 02 Jun 2019 23:51:54: 9000000 INFO @ Sun, 02 Jun 2019 23:51:57: 10000000 INFO @ Sun, 02 Jun 2019 23:52:02: 10000000 INFO @ Sun, 02 Jun 2019 23:52:02: 9000000 INFO @ Sun, 02 Jun 2019 23:52:05: 11000000 INFO @ Sun, 02 Jun 2019 23:52:09: 11000000 INFO @ Sun, 02 Jun 2019 23:52:11: 10000000 INFO @ Sun, 02 Jun 2019 23:52:13: 12000000 INFO @ Sun, 02 Jun 2019 23:52:17: 12000000 INFO @ Sun, 02 Jun 2019 23:52:20: 11000000 INFO @ Sun, 02 Jun 2019 23:52:20: 13000000 INFO @ Sun, 02 Jun 2019 23:52:25: 13000000 INFO @ Sun, 02 Jun 2019 23:52:27: 14000000 INFO @ Sun, 02 Jun 2019 23:52:28: 12000000 INFO @ Sun, 02 Jun 2019 23:52:33: 14000000 INFO @ Sun, 02 Jun 2019 23:52:34: 15000000 INFO @ Sun, 02 Jun 2019 23:52:37: 13000000 INFO @ Sun, 02 Jun 2019 23:52:40: 15000000 INFO @ Sun, 02 Jun 2019 23:52:41: 16000000 INFO @ Sun, 02 Jun 2019 23:52:45: 14000000 INFO @ Sun, 02 Jun 2019 23:52:48: 16000000 INFO @ Sun, 02 Jun 2019 23:52:49: 17000000 INFO @ Sun, 02 Jun 2019 23:52:54: 15000000 INFO @ Sun, 02 Jun 2019 23:52:56: 17000000 INFO @ Sun, 02 Jun 2019 23:52:56: 18000000 INFO @ Sun, 02 Jun 2019 23:53:01: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 23:53:01: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 23:53:01: #1 total tags in treatment: 18667445 INFO @ Sun, 02 Jun 2019 23:53:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:53:01: #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 23:53:02: #1 tags after filtering in treatment: 18667445 INFO @ Sun, 02 Jun 2019 23:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:53:02: #1 finished! INFO @ Sun, 02 Jun 2019 23:53:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:53:02: 16000000 INFO @ Sun, 02 Jun 2019 23:53:03: 18000000 INFO @ Sun, 02 Jun 2019 23:53:03: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 23:53:03: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 23:53:03: start model_add_line... INFO @ Sun, 02 Jun 2019 23:53:04: start X-correlation... INFO @ Sun, 02 Jun 2019 23:53:04: end of X-cor INFO @ Sun, 02 Jun 2019 23:53:04: #2 finished! INFO @ Sun, 02 Jun 2019 23:53:04: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:53:04: #2 alternative fragment length(s) may be 1,30,47,548,578 bps INFO @ Sun, 02 Jun 2019 23:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.10_model.r WARNING @ Sun, 02 Jun 2019 23:53:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:53:04: #2 You may need to consider one of the other alternative d(s): 1,30,47,548,578 WARNING @ Sun, 02 Jun 2019 23:53:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:53:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:53:10: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 23:53:10: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 23:53:10: #1 total tags in treatment: 18667445 INFO @ Sun, 02 Jun 2019 23:53:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:53:10: #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 23:53:10: #1 tags after filtering in treatment: 18667445 INFO @ Sun, 02 Jun 2019 23:53:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:53:10: #1 finished! INFO @ Sun, 02 Jun 2019 23:53:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:53:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:53:12: 17000000 INFO @ Sun, 02 Jun 2019 23:53:12: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 23:53:12: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 23:53:12: start model_add_line... INFO @ Sun, 02 Jun 2019 23:53:12: start X-correlation... INFO @ Sun, 02 Jun 2019 23:53:12: end of X-cor INFO @ Sun, 02 Jun 2019 23:53:12: #2 finished! INFO @ Sun, 02 Jun 2019 23:53:12: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:53:12: #2 alternative fragment length(s) may be 1,30,47,548,578 bps INFO @ Sun, 02 Jun 2019 23:53:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.20_model.r WARNING @ Sun, 02 Jun 2019 23:53:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:53:12: #2 You may need to consider one of the other alternative d(s): 1,30,47,548,578 WARNING @ Sun, 02 Jun 2019 23:53:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:53:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:53:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:53:20: 18000000 INFO @ Sun, 02 Jun 2019 23:53:26: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 23:53:26: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 23:53:26: #1 total tags in treatment: 18667445 INFO @ Sun, 02 Jun 2019 23:53:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:53:26: #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 23:53:27: #1 tags after filtering in treatment: 18667445 INFO @ Sun, 02 Jun 2019 23:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:53:27: #1 finished! INFO @ Sun, 02 Jun 2019 23:53:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:53:28: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 23:53:28: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 23:53:28: start model_add_line... INFO @ Sun, 02 Jun 2019 23:53:28: start X-correlation... INFO @ Sun, 02 Jun 2019 23:53:28: end of X-cor INFO @ Sun, 02 Jun 2019 23:53:28: #2 finished! INFO @ Sun, 02 Jun 2019 23:53:28: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 23:53:28: #2 alternative fragment length(s) may be 1,30,47,548,578 bps INFO @ Sun, 02 Jun 2019 23:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.05_model.r WARNING @ Sun, 02 Jun 2019 23:53:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:53:28: #2 You may need to consider one of the other alternative d(s): 1,30,47,548,578 WARNING @ Sun, 02 Jun 2019 23:53:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:53:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:53:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:53:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:53:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:54:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.10_summits.bed INFO @ Sun, 02 Jun 2019 23:54:05: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:54:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.20_summits.bed INFO @ Sun, 02 Jun 2019 23:54:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529223/SRX529223.05_summits.bed INFO @ Sun, 02 Jun 2019 23:54:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。