Job ID = 1294649 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:27:05 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 : 13,055,201 reads read : 13,055,201 reads written : 13,055,201 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: 00:05:09 13055201 reads; of these: 13055201 (100.00%) were unpaired; of these: 826485 (6.33%) aligned 0 times 8472060 (64.89%) aligned exactly 1 time 3756656 (28.78%) aligned >1 times 93.67% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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 8 files... [bam_rmdupse_core] 1176826 / 12228716 = 0.0962 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 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.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 09:43:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:43:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.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 09:43:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:43:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.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 09:43:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:43:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:43:11: 1000000 INFO @ Mon, 03 Jun 2019 09:43:11: 1000000 INFO @ Mon, 03 Jun 2019 09:43:12: 1000000 INFO @ Mon, 03 Jun 2019 09:43:18: 2000000 INFO @ Mon, 03 Jun 2019 09:43:18: 2000000 INFO @ Mon, 03 Jun 2019 09:43:19: 2000000 INFO @ Mon, 03 Jun 2019 09:43:25: 3000000 INFO @ Mon, 03 Jun 2019 09:43:26: 3000000 INFO @ Mon, 03 Jun 2019 09:43:26: 3000000 INFO @ Mon, 03 Jun 2019 09:43:31: 4000000 INFO @ Mon, 03 Jun 2019 09:43:33: 4000000 INFO @ Mon, 03 Jun 2019 09:43:33: 4000000 INFO @ Mon, 03 Jun 2019 09:43:38: 5000000 INFO @ Mon, 03 Jun 2019 09:43:40: 5000000 INFO @ Mon, 03 Jun 2019 09:43:40: 5000000 INFO @ Mon, 03 Jun 2019 09:43:45: 6000000 INFO @ Mon, 03 Jun 2019 09:43:47: 6000000 INFO @ Mon, 03 Jun 2019 09:43:47: 6000000 INFO @ Mon, 03 Jun 2019 09:43:51: 7000000 INFO @ Mon, 03 Jun 2019 09:43:54: 7000000 INFO @ Mon, 03 Jun 2019 09:43:55: 7000000 INFO @ Mon, 03 Jun 2019 09:43:58: 8000000 INFO @ Mon, 03 Jun 2019 09:44:02: 8000000 INFO @ Mon, 03 Jun 2019 09:44:02: 8000000 INFO @ Mon, 03 Jun 2019 09:44:05: 9000000 INFO @ Mon, 03 Jun 2019 09:44:09: 9000000 INFO @ Mon, 03 Jun 2019 09:44:09: 9000000 INFO @ Mon, 03 Jun 2019 09:44:12: 10000000 INFO @ Mon, 03 Jun 2019 09:44:16: 10000000 INFO @ Mon, 03 Jun 2019 09:44:16: 10000000 INFO @ Mon, 03 Jun 2019 09:44:19: 11000000 INFO @ Mon, 03 Jun 2019 09:44:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:44:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:44:19: #1 total tags in treatment: 11051890 INFO @ Mon, 03 Jun 2019 09:44:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:44:19: #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 09:44:19: #1 tags after filtering in treatment: 11051890 INFO @ Mon, 03 Jun 2019 09:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:44:19: #1 finished! INFO @ Mon, 03 Jun 2019 09:44:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:44:20: #2 number of paired peaks: 123 WARNING @ Mon, 03 Jun 2019 09:44:20: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Mon, 03 Jun 2019 09:44:20: start model_add_line... INFO @ Mon, 03 Jun 2019 09:44:20: start X-correlation... INFO @ Mon, 03 Jun 2019 09:44:20: end of X-cor INFO @ Mon, 03 Jun 2019 09:44:20: #2 finished! INFO @ Mon, 03 Jun 2019 09:44:20: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 09:44:20: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 09:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.05_model.r WARNING @ Mon, 03 Jun 2019 09:44:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:44:20: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 09:44:20: #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 09:44:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:44:23: 11000000 INFO @ Mon, 03 Jun 2019 09:44:23: 11000000 INFO @ Mon, 03 Jun 2019 09:44:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:44:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:44:24: #1 total tags in treatment: 11051890 INFO @ Mon, 03 Jun 2019 09:44:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:44:24: #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 09:44:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:44:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:44:24: #1 total tags in treatment: 11051890 INFO @ Mon, 03 Jun 2019 09:44:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:44:24: #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 09:44:24: #1 tags after filtering in treatment: 11051890 INFO @ Mon, 03 Jun 2019 09:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:44:24: #1 finished! INFO @ Mon, 03 Jun 2019 09:44:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:44:24: #1 tags after filtering in treatment: 11051890 INFO @ Mon, 03 Jun 2019 09:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:44:24: #1 finished! INFO @ Mon, 03 Jun 2019 09:44:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:44:25: #2 number of paired peaks: 123 WARNING @ Mon, 03 Jun 2019 09:44:25: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Mon, 03 Jun 2019 09:44:25: start model_add_line... INFO @ Mon, 03 Jun 2019 09:44:25: #2 number of paired peaks: 123 WARNING @ Mon, 03 Jun 2019 09:44:25: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Mon, 03 Jun 2019 09:44:25: start model_add_line... INFO @ Mon, 03 Jun 2019 09:44:25: start X-correlation... INFO @ Mon, 03 Jun 2019 09:44:25: end of X-cor INFO @ Mon, 03 Jun 2019 09:44:25: #2 finished! INFO @ Mon, 03 Jun 2019 09:44:25: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 09:44:25: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 09:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.20_model.r WARNING @ Mon, 03 Jun 2019 09:44:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:44:25: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 09:44:25: #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 09:44:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:44:25: start X-correlation... INFO @ Mon, 03 Jun 2019 09:44:25: end of X-cor INFO @ Mon, 03 Jun 2019 09:44:25: #2 finished! INFO @ Mon, 03 Jun 2019 09:44:25: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 09:44:25: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 09:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.10_model.r WARNING @ Mon, 03 Jun 2019 09:44:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:44:25: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 09:44:25: #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 09:44:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:44:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:44:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:44:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.05_summits.bed INFO @ Mon, 03 Jun 2019 09:45:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1788 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.20_summits.bed INFO @ Mon, 03 Jun 2019 09:45:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287800/SRX287800.10_summits.bed INFO @ Mon, 03 Jun 2019 09:45:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1205 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。