Job ID = 1294449 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:02:32 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 ) 2019-06-02T23:02:32 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 ) 2019-06-02T23:02:32 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 ) 2019-06-02T23:05:53 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 ) 2019-06-02T23:05:53 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 : 16,271,348 reads read : 16,271,348 reads written : 16,271,348 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: 00:08:56 16271348 reads; of these: 16271348 (100.00%) were unpaired; of these: 952440 (5.85%) aligned 0 times 8393940 (51.59%) aligned exactly 1 time 6924968 (42.56%) aligned >1 times 94.15% overall alignment rate Time searching: 00:08:56 Overall time: 00:08:56 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] 2151147 / 15318908 = 0.1404 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 08:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.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 08:21:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.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 08:21:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.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 08:21:04: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:04: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:14: 1000000 INFO @ Mon, 03 Jun 2019 08:21:15: 1000000 INFO @ Mon, 03 Jun 2019 08:21:15: 1000000 INFO @ Mon, 03 Jun 2019 08:21:24: 2000000 INFO @ Mon, 03 Jun 2019 08:21:25: 2000000 INFO @ Mon, 03 Jun 2019 08:21:25: 2000000 INFO @ Mon, 03 Jun 2019 08:21:34: 3000000 INFO @ Mon, 03 Jun 2019 08:21:35: 3000000 INFO @ Mon, 03 Jun 2019 08:21:35: 3000000 INFO @ Mon, 03 Jun 2019 08:21:43: 4000000 INFO @ Mon, 03 Jun 2019 08:21:45: 4000000 INFO @ Mon, 03 Jun 2019 08:21:45: 4000000 INFO @ Mon, 03 Jun 2019 08:21:52: 5000000 INFO @ Mon, 03 Jun 2019 08:21:55: 5000000 INFO @ Mon, 03 Jun 2019 08:21:55: 5000000 INFO @ Mon, 03 Jun 2019 08:22:02: 6000000 INFO @ Mon, 03 Jun 2019 08:22:05: 6000000 INFO @ Mon, 03 Jun 2019 08:22:05: 6000000 INFO @ Mon, 03 Jun 2019 08:22:11: 7000000 INFO @ Mon, 03 Jun 2019 08:22:15: 7000000 INFO @ Mon, 03 Jun 2019 08:22:15: 7000000 INFO @ Mon, 03 Jun 2019 08:22:20: 8000000 INFO @ Mon, 03 Jun 2019 08:22:24: 8000000 INFO @ Mon, 03 Jun 2019 08:22:24: 8000000 INFO @ Mon, 03 Jun 2019 08:22:30: 9000000 INFO @ Mon, 03 Jun 2019 08:22:33: 9000000 INFO @ Mon, 03 Jun 2019 08:22:33: 9000000 INFO @ Mon, 03 Jun 2019 08:22:40: 10000000 INFO @ Mon, 03 Jun 2019 08:22:43: 10000000 INFO @ Mon, 03 Jun 2019 08:22:43: 10000000 INFO @ Mon, 03 Jun 2019 08:22:49: 11000000 INFO @ Mon, 03 Jun 2019 08:22:51: 11000000 INFO @ Mon, 03 Jun 2019 08:22:52: 11000000 INFO @ Mon, 03 Jun 2019 08:22:59: 12000000 INFO @ Mon, 03 Jun 2019 08:23:00: 12000000 INFO @ Mon, 03 Jun 2019 08:23:00: 12000000 INFO @ Mon, 03 Jun 2019 08:23:07: 13000000 INFO @ Mon, 03 Jun 2019 08:23:08: 13000000 INFO @ Mon, 03 Jun 2019 08:23:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:08: #1 total tags in treatment: 13167761 INFO @ Mon, 03 Jun 2019 08:23:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:08: #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 08:23:09: #1 tags after filtering in treatment: 13167761 INFO @ Mon, 03 Jun 2019 08:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:09: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:09: #1 total tags in treatment: 13167761 INFO @ Mon, 03 Jun 2019 08:23:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:09: #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 08:23:09: #1 tags after filtering in treatment: 13167761 INFO @ Mon, 03 Jun 2019 08:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:09: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:10: 13000000 INFO @ Mon, 03 Jun 2019 08:23:10: #2 number of paired peaks: 387 WARNING @ Mon, 03 Jun 2019 08:23:10: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 03 Jun 2019 08:23:10: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:10: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:10: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:10: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:10: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:23:10: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.05_model.r WARNING @ Mon, 03 Jun 2019 08:23:10: #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 08:23:10: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:23:10: #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 08:23:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:10: #2 number of paired peaks: 387 WARNING @ Mon, 03 Jun 2019 08:23:10: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 03 Jun 2019 08:23:10: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:10: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:10: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:10: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:10: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:23:10: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.10_model.r WARNING @ Mon, 03 Jun 2019 08:23:10: #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 08:23:10: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:23:10: #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 08:23:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:23:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:23:11: #1 total tags in treatment: 13167761 INFO @ Mon, 03 Jun 2019 08:23:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:23:11: #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 08:23:12: #1 tags after filtering in treatment: 13167761 INFO @ Mon, 03 Jun 2019 08:23:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:23:12: #1 finished! INFO @ Mon, 03 Jun 2019 08:23:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:23:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:23:13: #2 number of paired peaks: 387 WARNING @ Mon, 03 Jun 2019 08:23:13: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Mon, 03 Jun 2019 08:23:13: start model_add_line... INFO @ Mon, 03 Jun 2019 08:23:13: start X-correlation... INFO @ Mon, 03 Jun 2019 08:23:13: end of X-cor INFO @ Mon, 03 Jun 2019 08:23:13: #2 finished! INFO @ Mon, 03 Jun 2019 08:23:13: #2 predicted fragment length is 47 bps INFO @ Mon, 03 Jun 2019 08:23:13: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 03 Jun 2019 08:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.20_model.r WARNING @ Mon, 03 Jun 2019 08:23:13: #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 08:23:13: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 03 Jun 2019 08:23:13: #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 08:23:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:23:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:23:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:23:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.05_summits.bed INFO @ Mon, 03 Jun 2019 08:24:04: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2429 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.10_summits.bed INFO @ Mon, 03 Jun 2019 08:24:05: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1623 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287655/SRX287655.20_summits.bed INFO @ Mon, 03 Jun 2019 08:24:08: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1143 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。