Job ID = 1293001 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:22:53 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 ) 2019-06-02T12:22:53 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 : 19,467,594 reads read : 38,935,188 reads written : 19,467,594 reads 0-length : 19,467,594 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: 00:07:06 19467594 reads; of these: 19467594 (100.00%) were unpaired; of these: 760327 (3.91%) aligned 0 times 15555488 (79.90%) aligned exactly 1 time 3151779 (16.19%) aligned >1 times 96.09% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 8 files... [bam_rmdupse_core] 3061194 / 18707267 = 0.1636 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 21:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.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 21:39:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:39:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.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 21:39:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:39:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.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 21:39:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:39:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:39:25: 1000000 INFO @ Sun, 02 Jun 2019 21:39:26: 1000000 INFO @ Sun, 02 Jun 2019 21:39:28: 1000000 INFO @ Sun, 02 Jun 2019 21:39:33: 2000000 INFO @ Sun, 02 Jun 2019 21:39:35: 2000000 INFO @ Sun, 02 Jun 2019 21:39:39: 2000000 INFO @ Sun, 02 Jun 2019 21:39:41: 3000000 INFO @ Sun, 02 Jun 2019 21:39:43: 3000000 INFO @ Sun, 02 Jun 2019 21:39:48: 4000000 INFO @ Sun, 02 Jun 2019 21:39:50: 3000000 INFO @ Sun, 02 Jun 2019 21:39:51: 4000000 INFO @ Sun, 02 Jun 2019 21:39:56: 5000000 INFO @ Sun, 02 Jun 2019 21:40:00: 5000000 INFO @ Sun, 02 Jun 2019 21:40:01: 4000000 INFO @ Sun, 02 Jun 2019 21:40:04: 6000000 INFO @ Sun, 02 Jun 2019 21:40:08: 6000000 INFO @ Sun, 02 Jun 2019 21:40:11: 7000000 INFO @ Sun, 02 Jun 2019 21:40:12: 5000000 INFO @ Sun, 02 Jun 2019 21:40:17: 7000000 INFO @ Sun, 02 Jun 2019 21:40:19: 8000000 INFO @ Sun, 02 Jun 2019 21:40:23: 6000000 INFO @ Sun, 02 Jun 2019 21:40:25: 8000000 INFO @ Sun, 02 Jun 2019 21:40:26: 9000000 INFO @ Sun, 02 Jun 2019 21:40:33: 9000000 INFO @ Sun, 02 Jun 2019 21:40:34: 10000000 INFO @ Sun, 02 Jun 2019 21:40:34: 7000000 INFO @ Sun, 02 Jun 2019 21:40:41: 11000000 INFO @ Sun, 02 Jun 2019 21:40:41: 10000000 INFO @ Sun, 02 Jun 2019 21:40:44: 8000000 INFO @ Sun, 02 Jun 2019 21:40:49: 12000000 INFO @ Sun, 02 Jun 2019 21:40:50: 11000000 INFO @ Sun, 02 Jun 2019 21:40:54: 9000000 INFO @ Sun, 02 Jun 2019 21:40:56: 13000000 INFO @ Sun, 02 Jun 2019 21:40:58: 12000000 INFO @ Sun, 02 Jun 2019 21:41:03: 14000000 INFO @ Sun, 02 Jun 2019 21:41:04: 10000000 INFO @ Sun, 02 Jun 2019 21:41:05: 13000000 INFO @ Sun, 02 Jun 2019 21:41:11: 15000000 INFO @ Sun, 02 Jun 2019 21:41:13: 14000000 INFO @ Sun, 02 Jun 2019 21:41:14: 11000000 INFO @ Sun, 02 Jun 2019 21:41:16: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:41:16: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:41:16: #1 total tags in treatment: 15646073 INFO @ Sun, 02 Jun 2019 21:41:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:41:16: #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 21:41:17: #1 tags after filtering in treatment: 15646073 INFO @ Sun, 02 Jun 2019 21:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:41:17: #1 finished! INFO @ Sun, 02 Jun 2019 21:41:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:41:18: #2 number of paired peaks: 315 WARNING @ Sun, 02 Jun 2019 21:41:18: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sun, 02 Jun 2019 21:41:18: start model_add_line... INFO @ Sun, 02 Jun 2019 21:41:18: start X-correlation... INFO @ Sun, 02 Jun 2019 21:41:18: end of X-cor INFO @ Sun, 02 Jun 2019 21:41:18: #2 finished! INFO @ Sun, 02 Jun 2019 21:41:18: #2 predicted fragment length is 79 bps INFO @ Sun, 02 Jun 2019 21:41:18: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 02 Jun 2019 21:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.10_model.r WARNING @ Sun, 02 Jun 2019 21:41:18: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:41:18: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 02 Jun 2019 21:41:18: #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 21:41:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:41:20: 15000000 INFO @ Sun, 02 Jun 2019 21:41:24: 12000000 INFO @ Sun, 02 Jun 2019 21:41:25: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:41:25: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:41:25: #1 total tags in treatment: 15646073 INFO @ Sun, 02 Jun 2019 21:41:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:41:25: #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 21:41:26: #1 tags after filtering in treatment: 15646073 INFO @ Sun, 02 Jun 2019 21:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:41:26: #1 finished! INFO @ Sun, 02 Jun 2019 21:41:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:41:27: #2 number of paired peaks: 315 WARNING @ Sun, 02 Jun 2019 21:41:27: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sun, 02 Jun 2019 21:41:27: start model_add_line... INFO @ Sun, 02 Jun 2019 21:41:27: start X-correlation... INFO @ Sun, 02 Jun 2019 21:41:27: end of X-cor INFO @ Sun, 02 Jun 2019 21:41:27: #2 finished! INFO @ Sun, 02 Jun 2019 21:41:27: #2 predicted fragment length is 79 bps INFO @ Sun, 02 Jun 2019 21:41:27: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 02 Jun 2019 21:41:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.20_model.r WARNING @ Sun, 02 Jun 2019 21:41:27: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:41:27: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 02 Jun 2019 21:41:27: #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 21:41:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:41:34: 13000000 INFO @ Sun, 02 Jun 2019 21:41:44: 14000000 INFO @ Sun, 02 Jun 2019 21:41:54: 15000000 INFO @ Sun, 02 Jun 2019 21:41:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:42:00: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:42:00: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:42:00: #1 total tags in treatment: 15646073 INFO @ Sun, 02 Jun 2019 21:42:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:42:00: #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 21:42:00: #1 tags after filtering in treatment: 15646073 INFO @ Sun, 02 Jun 2019 21:42:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:42:00: #1 finished! INFO @ Sun, 02 Jun 2019 21:42:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:42:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:42:01: #2 number of paired peaks: 315 WARNING @ Sun, 02 Jun 2019 21:42:01: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sun, 02 Jun 2019 21:42:01: start model_add_line... INFO @ Sun, 02 Jun 2019 21:42:02: start X-correlation... INFO @ Sun, 02 Jun 2019 21:42:02: end of X-cor INFO @ Sun, 02 Jun 2019 21:42:02: #2 finished! INFO @ Sun, 02 Jun 2019 21:42:02: #2 predicted fragment length is 79 bps INFO @ Sun, 02 Jun 2019 21:42:02: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sun, 02 Jun 2019 21:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.05_model.r WARNING @ Sun, 02 Jun 2019 21:42:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:42:02: #2 You may need to consider one of the other alternative d(s): 4,79 WARNING @ Sun, 02 Jun 2019 21:42:02: #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 21:42:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:42:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:42:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:42:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.10_summits.bed INFO @ Sun, 02 Jun 2019 21:42:16: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1452 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.20_summits.bed INFO @ Sun, 02 Jun 2019 21:42:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (648 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:42:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020775/SRX5020775.05_summits.bed INFO @ Sun, 02 Jun 2019 21:43:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2688 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。