Job ID = 1294423 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:36:10 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 ) 2019-06-02T22:36:10 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 ) 2019-06-02T22:36:10 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 : 21,266,404 reads read : 21,266,404 reads written : 21,266,404 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: 00:09:24 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1402718 (6.60%) aligned 0 times 13365639 (62.85%) aligned exactly 1 time 6498047 (30.56%) aligned >1 times 93.40% overall alignment rate Time searching: 00:09:24 Overall time: 00:09:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3845876 / 19863686 = 0.1936 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, 03 Jun 2019 08:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 08:00:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 08:00:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 08:00:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:00:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:00:37: 1000000 INFO @ Mon, 03 Jun 2019 08:00:39: 1000000 INFO @ Mon, 03 Jun 2019 08:00:40: 1000000 INFO @ Mon, 03 Jun 2019 08:00:44: 2000000 INFO @ Mon, 03 Jun 2019 08:00:46: 2000000 INFO @ Mon, 03 Jun 2019 08:00:48: 2000000 INFO @ Mon, 03 Jun 2019 08:00:50: 3000000 INFO @ Mon, 03 Jun 2019 08:00:53: 3000000 INFO @ Mon, 03 Jun 2019 08:00:56: 3000000 INFO @ Mon, 03 Jun 2019 08:00:57: 4000000 INFO @ Mon, 03 Jun 2019 08:01:02: 4000000 INFO @ Mon, 03 Jun 2019 08:01:03: 5000000 INFO @ Mon, 03 Jun 2019 08:01:04: 4000000 INFO @ Mon, 03 Jun 2019 08:01:09: 5000000 INFO @ Mon, 03 Jun 2019 08:01:10: 6000000 INFO @ Mon, 03 Jun 2019 08:01:12: 5000000 INFO @ Mon, 03 Jun 2019 08:01:16: 6000000 INFO @ Mon, 03 Jun 2019 08:01:16: 7000000 INFO @ Mon, 03 Jun 2019 08:01:19: 6000000 INFO @ Mon, 03 Jun 2019 08:01:22: 8000000 INFO @ Mon, 03 Jun 2019 08:01:23: 7000000 INFO @ Mon, 03 Jun 2019 08:01:26: 7000000 INFO @ Mon, 03 Jun 2019 08:01:29: 9000000 INFO @ Mon, 03 Jun 2019 08:01:31: 8000000 INFO @ Mon, 03 Jun 2019 08:01:33: 8000000 INFO @ Mon, 03 Jun 2019 08:01:35: 10000000 INFO @ Mon, 03 Jun 2019 08:01:38: 9000000 INFO @ Mon, 03 Jun 2019 08:01:40: 9000000 INFO @ Mon, 03 Jun 2019 08:01:42: 11000000 INFO @ Mon, 03 Jun 2019 08:01:45: 10000000 INFO @ Mon, 03 Jun 2019 08:01:47: 10000000 INFO @ Mon, 03 Jun 2019 08:01:48: 12000000 INFO @ Mon, 03 Jun 2019 08:01:53: 11000000 INFO @ Mon, 03 Jun 2019 08:01:55: 13000000 INFO @ Mon, 03 Jun 2019 08:01:55: 11000000 INFO @ Mon, 03 Jun 2019 08:02:00: 12000000 INFO @ Mon, 03 Jun 2019 08:02:01: 14000000 INFO @ Mon, 03 Jun 2019 08:02:03: 12000000 INFO @ Mon, 03 Jun 2019 08:02:07: 13000000 INFO @ Mon, 03 Jun 2019 08:02:08: 15000000 INFO @ Mon, 03 Jun 2019 08:02:10: 13000000 INFO @ Mon, 03 Jun 2019 08:02:14: 14000000 INFO @ Mon, 03 Jun 2019 08:02:14: 16000000 INFO @ Mon, 03 Jun 2019 08:02:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:02:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:02:15: #1 total tags in treatment: 16017810 INFO @ Mon, 03 Jun 2019 08:02:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:02:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:02:15: #1 tags after filtering in treatment: 16017810 INFO @ Mon, 03 Jun 2019 08:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:02:15: #1 finished! INFO @ Mon, 03 Jun 2019 08:02:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:02:16: #2 number of paired peaks: 234 WARNING @ Mon, 03 Jun 2019 08:02:16: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Mon, 03 Jun 2019 08:02:16: start model_add_line... INFO @ Mon, 03 Jun 2019 08:02:16: start X-correlation... INFO @ Mon, 03 Jun 2019 08:02:16: end of X-cor INFO @ Mon, 03 Jun 2019 08:02:16: #2 finished! INFO @ Mon, 03 Jun 2019 08:02:16: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:02:16: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:02:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.05_model.r WARNING @ Mon, 03 Jun 2019 08:02:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:02:16: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:02:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:02:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:02:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:02:17: 14000000 INFO @ Mon, 03 Jun 2019 08:02:21: 15000000 INFO @ Mon, 03 Jun 2019 08:02:24: 15000000 INFO @ Mon, 03 Jun 2019 08:02:28: 16000000 INFO @ Mon, 03 Jun 2019 08:02:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:02:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:02:28: #1 total tags in treatment: 16017810 INFO @ Mon, 03 Jun 2019 08:02:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:02:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:02:29: #1 tags after filtering in treatment: 16017810 INFO @ Mon, 03 Jun 2019 08:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:02:29: #1 finished! INFO @ Mon, 03 Jun 2019 08:02:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:02:30: #2 number of paired peaks: 234 WARNING @ Mon, 03 Jun 2019 08:02:30: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Mon, 03 Jun 2019 08:02:30: start model_add_line... INFO @ Mon, 03 Jun 2019 08:02:30: start X-correlation... INFO @ Mon, 03 Jun 2019 08:02:30: end of X-cor INFO @ Mon, 03 Jun 2019 08:02:30: #2 finished! INFO @ Mon, 03 Jun 2019 08:02:30: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:02:30: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.20_model.r WARNING @ Mon, 03 Jun 2019 08:02:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:02:30: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:02:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:02:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:02:31: 16000000 INFO @ Mon, 03 Jun 2019 08:02:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:02:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:02:31: #1 total tags in treatment: 16017810 INFO @ Mon, 03 Jun 2019 08:02:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:02:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:02:32: #1 tags after filtering in treatment: 16017810 INFO @ Mon, 03 Jun 2019 08:02:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:02:32: #1 finished! INFO @ Mon, 03 Jun 2019 08:02:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:02:33: #2 number of paired peaks: 234 WARNING @ Mon, 03 Jun 2019 08:02:33: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Mon, 03 Jun 2019 08:02:33: start model_add_line... INFO @ Mon, 03 Jun 2019 08:02:33: start X-correlation... INFO @ Mon, 03 Jun 2019 08:02:33: end of X-cor INFO @ Mon, 03 Jun 2019 08:02:33: #2 finished! INFO @ Mon, 03 Jun 2019 08:02:33: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:02:33: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.10_model.r WARNING @ Mon, 03 Jun 2019 08:02:33: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:02:33: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:02:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:02:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:02:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:03:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:03:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.05_summits.bed INFO @ Mon, 03 Jun 2019 08:03:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2053 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.20_summits.bed INFO @ Mon, 03 Jun 2019 08:03:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287594/SRX287594.10_summits.bed INFO @ Mon, 03 Jun 2019 08:03:36: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1737 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。