Job ID = 1295120 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:01:19 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 ) 2019-06-03T03:02:52 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 ) 2019-06-03T03:02:52 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 ) 2019-06-03T03:11:58 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 ) 2019-06-03T03:23:48 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 ) 2019-06-03T03:23:48 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 : 61,296,665 reads read : 61,296,665 reads written : 61,296,665 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: 00:21:07 61296665 reads; of these: 61296665 (100.00%) were unpaired; of these: 4910737 (8.01%) aligned 0 times 45436620 (74.13%) aligned exactly 1 time 10949308 (17.86%) aligned >1 times 91.99% overall alignment rate Time searching: 00:21:07 Overall time: 00:21:07 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 20 files... [bam_rmdupse_core] 42814728 / 56385928 = 0.7593 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 12:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.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 12:57:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:57:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.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 12:57:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:57:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.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 12:57:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:57:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:57:30: 1000000 INFO @ Mon, 03 Jun 2019 12:57:31: 1000000 INFO @ Mon, 03 Jun 2019 12:57:31: 1000000 INFO @ Mon, 03 Jun 2019 12:57:38: 2000000 INFO @ Mon, 03 Jun 2019 12:57:39: 2000000 INFO @ Mon, 03 Jun 2019 12:57:40: 2000000 INFO @ Mon, 03 Jun 2019 12:57:46: 3000000 INFO @ Mon, 03 Jun 2019 12:57:46: 3000000 INFO @ Mon, 03 Jun 2019 12:57:48: 3000000 INFO @ Mon, 03 Jun 2019 12:57:55: 4000000 INFO @ Mon, 03 Jun 2019 12:57:55: 4000000 INFO @ Mon, 03 Jun 2019 12:57:57: 4000000 INFO @ Mon, 03 Jun 2019 12:58:05: 5000000 INFO @ Mon, 03 Jun 2019 12:58:06: 5000000 INFO @ Mon, 03 Jun 2019 12:58:07: 5000000 INFO @ Mon, 03 Jun 2019 12:58:16: 6000000 INFO @ Mon, 03 Jun 2019 12:58:16: 6000000 INFO @ Mon, 03 Jun 2019 12:58:17: 6000000 INFO @ Mon, 03 Jun 2019 12:58:26: 7000000 INFO @ Mon, 03 Jun 2019 12:58:26: 7000000 INFO @ Mon, 03 Jun 2019 12:58:27: 7000000 INFO @ Mon, 03 Jun 2019 12:58:35: 8000000 INFO @ Mon, 03 Jun 2019 12:58:36: 8000000 INFO @ Mon, 03 Jun 2019 12:58:36: 8000000 INFO @ Mon, 03 Jun 2019 12:58:45: 9000000 INFO @ Mon, 03 Jun 2019 12:58:46: 9000000 INFO @ Mon, 03 Jun 2019 12:58:46: 9000000 INFO @ Mon, 03 Jun 2019 12:58:54: 10000000 INFO @ Mon, 03 Jun 2019 12:58:55: 10000000 INFO @ Mon, 03 Jun 2019 12:58:56: 10000000 INFO @ Mon, 03 Jun 2019 12:59:04: 11000000 INFO @ Mon, 03 Jun 2019 12:59:06: 11000000 INFO @ Mon, 03 Jun 2019 12:59:06: 11000000 INFO @ Mon, 03 Jun 2019 12:59:14: 12000000 INFO @ Mon, 03 Jun 2019 12:59:16: 12000000 INFO @ Mon, 03 Jun 2019 12:59:16: 12000000 INFO @ Mon, 03 Jun 2019 12:59:23: 13000000 INFO @ Mon, 03 Jun 2019 12:59:25: 13000000 INFO @ Mon, 03 Jun 2019 12:59:26: 13000000 INFO @ Mon, 03 Jun 2019 12:59:28: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 12:59:28: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 12:59:28: #1 total tags in treatment: 13571200 INFO @ Mon, 03 Jun 2019 12:59:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:59:28: #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 12:59:29: #1 tags after filtering in treatment: 13571200 INFO @ Mon, 03 Jun 2019 12:59:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:59:29: #1 finished! INFO @ Mon, 03 Jun 2019 12:59:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:59:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:59:30: #2 number of paired peaks: 370 WARNING @ Mon, 03 Jun 2019 12:59:30: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Mon, 03 Jun 2019 12:59:30: start model_add_line... INFO @ Mon, 03 Jun 2019 12:59:30: start X-correlation... INFO @ Mon, 03 Jun 2019 12:59:30: end of X-cor INFO @ Mon, 03 Jun 2019 12:59:30: #2 finished! INFO @ Mon, 03 Jun 2019 12:59:30: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 12:59:30: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 12:59:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.10_model.r WARNING @ Mon, 03 Jun 2019 12:59:30: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:59:30: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 12:59:30: #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 12:59:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:59:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:59:31: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 12:59:31: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 12:59:31: #1 total tags in treatment: 13571200 INFO @ Mon, 03 Jun 2019 12:59:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:59:31: #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 12:59:31: #1 tags after filtering in treatment: 13571200 INFO @ Mon, 03 Jun 2019 12:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:59:31: #1 finished! INFO @ Mon, 03 Jun 2019 12:59:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:59:32: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 12:59:32: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 12:59:32: #1 total tags in treatment: 13571200 INFO @ Mon, 03 Jun 2019 12:59:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:59:32: #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 12:59:32: #1 tags after filtering in treatment: 13571200 INFO @ Mon, 03 Jun 2019 12:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:59:32: #1 finished! INFO @ Mon, 03 Jun 2019 12:59:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:59:32: #2 number of paired peaks: 370 WARNING @ Mon, 03 Jun 2019 12:59:32: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Mon, 03 Jun 2019 12:59:32: start model_add_line... INFO @ Mon, 03 Jun 2019 12:59:32: start X-correlation... INFO @ Mon, 03 Jun 2019 12:59:32: end of X-cor INFO @ Mon, 03 Jun 2019 12:59:32: #2 finished! INFO @ Mon, 03 Jun 2019 12:59:32: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 12:59:32: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 12:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.05_model.r WARNING @ Mon, 03 Jun 2019 12:59:32: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:59:32: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 12:59:32: #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 12:59:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:59:33: #2 number of paired peaks: 370 WARNING @ Mon, 03 Jun 2019 12:59:33: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Mon, 03 Jun 2019 12:59:33: start model_add_line... INFO @ Mon, 03 Jun 2019 12:59:34: start X-correlation... INFO @ Mon, 03 Jun 2019 12:59:34: end of X-cor INFO @ Mon, 03 Jun 2019 12:59:34: #2 finished! INFO @ Mon, 03 Jun 2019 12:59:34: #2 predicted fragment length is 41 bps INFO @ Mon, 03 Jun 2019 12:59:34: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 03 Jun 2019 12:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.20_model.r WARNING @ Mon, 03 Jun 2019 12:59:34: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:59:34: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 03 Jun 2019 12:59:34: #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 12:59:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:00:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:00:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:00:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.10_summits.bed INFO @ Mon, 03 Jun 2019 13:00:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3104 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.05_summits.bed INFO @ Mon, 03 Jun 2019 13:00:28: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12782 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320156/SRX320156.20_summits.bed INFO @ Mon, 03 Jun 2019 13:00:30: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (836 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。