Job ID = 1294180 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:20:37 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 : 28,671,012 reads read : 28,671,012 reads written : 28,671,012 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: 00:10:26 28671012 reads; of these: 28671012 (100.00%) were unpaired; of these: 2599963 (9.07%) aligned 0 times 17962550 (62.65%) aligned exactly 1 time 8108499 (28.28%) aligned >1 times 90.93% overall alignment rate Time searching: 00:10:26 Overall time: 00:10:26 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] 9034991 / 26071049 = 0.3466 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 05:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.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 05:37:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:37:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.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 05:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.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 05:37:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:37:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:37:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:37:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:37:58: 1000000 INFO @ Mon, 03 Jun 2019 05:37:58: 1000000 INFO @ Mon, 03 Jun 2019 05:37:59: 1000000 INFO @ Mon, 03 Jun 2019 05:38:07: 2000000 INFO @ Mon, 03 Jun 2019 05:38:07: 2000000 INFO @ Mon, 03 Jun 2019 05:38:07: 2000000 INFO @ Mon, 03 Jun 2019 05:38:15: 3000000 INFO @ Mon, 03 Jun 2019 05:38:15: 3000000 INFO @ Mon, 03 Jun 2019 05:38:15: 3000000 INFO @ Mon, 03 Jun 2019 05:38:23: 4000000 INFO @ Mon, 03 Jun 2019 05:38:23: 4000000 INFO @ Mon, 03 Jun 2019 05:38:23: 4000000 INFO @ Mon, 03 Jun 2019 05:38:31: 5000000 INFO @ Mon, 03 Jun 2019 05:38:31: 5000000 INFO @ Mon, 03 Jun 2019 05:38:31: 5000000 INFO @ Mon, 03 Jun 2019 05:38:39: 6000000 INFO @ Mon, 03 Jun 2019 05:38:39: 6000000 INFO @ Mon, 03 Jun 2019 05:38:39: 6000000 INFO @ Mon, 03 Jun 2019 05:38:47: 7000000 INFO @ Mon, 03 Jun 2019 05:38:47: 7000000 INFO @ Mon, 03 Jun 2019 05:38:48: 7000000 INFO @ Mon, 03 Jun 2019 05:38:55: 8000000 INFO @ Mon, 03 Jun 2019 05:38:56: 8000000 INFO @ Mon, 03 Jun 2019 05:38:57: 8000000 INFO @ Mon, 03 Jun 2019 05:39:03: 9000000 INFO @ Mon, 03 Jun 2019 05:39:04: 9000000 INFO @ Mon, 03 Jun 2019 05:39:05: 9000000 INFO @ Mon, 03 Jun 2019 05:39:12: 10000000 INFO @ Mon, 03 Jun 2019 05:39:12: 10000000 INFO @ Mon, 03 Jun 2019 05:39:13: 10000000 INFO @ Mon, 03 Jun 2019 05:39:20: 11000000 INFO @ Mon, 03 Jun 2019 05:39:20: 11000000 INFO @ Mon, 03 Jun 2019 05:39:21: 11000000 INFO @ Mon, 03 Jun 2019 05:39:28: 12000000 INFO @ Mon, 03 Jun 2019 05:39:28: 12000000 INFO @ Mon, 03 Jun 2019 05:39:29: 12000000 INFO @ Mon, 03 Jun 2019 05:39:36: 13000000 INFO @ Mon, 03 Jun 2019 05:39:36: 13000000 INFO @ Mon, 03 Jun 2019 05:39:37: 13000000 INFO @ Mon, 03 Jun 2019 05:39:44: 14000000 INFO @ Mon, 03 Jun 2019 05:39:44: 14000000 INFO @ Mon, 03 Jun 2019 05:39:45: 14000000 INFO @ Mon, 03 Jun 2019 05:39:52: 15000000 INFO @ Mon, 03 Jun 2019 05:39:52: 15000000 INFO @ Mon, 03 Jun 2019 05:39:53: 15000000 INFO @ Mon, 03 Jun 2019 05:40:00: 16000000 INFO @ Mon, 03 Jun 2019 05:40:00: 16000000 INFO @ Mon, 03 Jun 2019 05:40:01: 16000000 INFO @ Mon, 03 Jun 2019 05:40:08: 17000000 INFO @ Mon, 03 Jun 2019 05:40:09: 17000000 INFO @ Mon, 03 Jun 2019 05:40:09: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:40:09: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:40:09: #1 total tags in treatment: 17036058 INFO @ Mon, 03 Jun 2019 05:40:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:09: #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 05:40:09: 17000000 INFO @ Mon, 03 Jun 2019 05:40:09: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:40:09: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:40:09: #1 total tags in treatment: 17036058 INFO @ Mon, 03 Jun 2019 05:40:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:09: #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 05:40:09: #1 tags after filtering in treatment: 17036058 INFO @ Mon, 03 Jun 2019 05:40:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:09: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:09: #1 tags after filtering in treatment: 17036058 INFO @ Mon, 03 Jun 2019 05:40:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:09: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:09: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:40:09: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:40:09: #1 total tags in treatment: 17036058 INFO @ Mon, 03 Jun 2019 05:40:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:09: #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 05:40:10: #1 tags after filtering in treatment: 17036058 INFO @ Mon, 03 Jun 2019 05:40:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:10: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:11: #2 number of paired peaks: 823 WARNING @ Mon, 03 Jun 2019 05:40:11: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Mon, 03 Jun 2019 05:40:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:40:11: #2 number of paired peaks: 823 WARNING @ Mon, 03 Jun 2019 05:40:11: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Mon, 03 Jun 2019 05:40:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:40:11: start X-correlation... INFO @ Mon, 03 Jun 2019 05:40:11: end of X-cor INFO @ Mon, 03 Jun 2019 05:40:11: #2 finished! INFO @ Mon, 03 Jun 2019 05:40:11: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 05:40:11: #2 alternative fragment length(s) may be 4,47 bps INFO @ Mon, 03 Jun 2019 05:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.20_model.r WARNING @ Mon, 03 Jun 2019 05:40:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:40:11: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Mon, 03 Jun 2019 05:40:11: #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 05:40:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:40:11: start X-correlation... INFO @ Mon, 03 Jun 2019 05:40:11: end of X-cor INFO @ Mon, 03 Jun 2019 05:40:11: #2 finished! INFO @ Mon, 03 Jun 2019 05:40:11: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 05:40:11: #2 alternative fragment length(s) may be 4,47 bps INFO @ Mon, 03 Jun 2019 05:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.05_model.r WARNING @ Mon, 03 Jun 2019 05:40:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:40:11: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Mon, 03 Jun 2019 05:40:11: #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 05:40:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:40:11: #2 number of paired peaks: 823 WARNING @ Mon, 03 Jun 2019 05:40:11: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Mon, 03 Jun 2019 05:40:11: start model_add_line... INFO @ Mon, 03 Jun 2019 05:40:11: start X-correlation... INFO @ Mon, 03 Jun 2019 05:40:11: end of X-cor INFO @ Mon, 03 Jun 2019 05:40:11: #2 finished! INFO @ Mon, 03 Jun 2019 05:40:11: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 05:40:11: #2 alternative fragment length(s) may be 4,47 bps INFO @ Mon, 03 Jun 2019 05:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.10_model.r WARNING @ Mon, 03 Jun 2019 05:40:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:40:11: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Mon, 03 Jun 2019 05:40:11: #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 05:40:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:40:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:40:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:40:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.20_summits.bed INFO @ Mon, 03 Jun 2019 05:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.05_summits.bed INFO @ Mon, 03 Jun 2019 05:41:18: Done! INFO @ Mon, 03 Jun 2019 05:41:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2341 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4882 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197568/SRX197568.10_summits.bed INFO @ Mon, 03 Jun 2019 05:41:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3438 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。