Job ID = 1306793 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T12:56:39 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 ) 2019-06-03T12:57:38 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 ) 2019-06-03T12:57:38 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 : 6,705,346 reads read : 6,705,346 reads written : 6,705,346 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: 00:03:18 6705346 reads; of these: 6705346 (100.00%) were unpaired; of these: 306026 (4.56%) aligned 0 times 3670059 (54.73%) aligned exactly 1 time 2729261 (40.70%) aligned >1 times 95.44% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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_rmdupse_core] 800925 / 6399320 = 0.1252 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 22:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.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 22:04:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:04:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.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 22:04:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:04:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.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 22:04:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:04:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:04:55: 1000000 INFO @ Mon, 03 Jun 2019 22:04:55: 1000000 INFO @ Mon, 03 Jun 2019 22:04:56: 1000000 INFO @ Mon, 03 Jun 2019 22:05:03: 2000000 INFO @ Mon, 03 Jun 2019 22:05:03: 2000000 INFO @ Mon, 03 Jun 2019 22:05:05: 2000000 INFO @ Mon, 03 Jun 2019 22:05:10: 3000000 INFO @ Mon, 03 Jun 2019 22:05:11: 3000000 INFO @ Mon, 03 Jun 2019 22:05:13: 3000000 INFO @ Mon, 03 Jun 2019 22:05:18: 4000000 INFO @ Mon, 03 Jun 2019 22:05:18: 4000000 INFO @ Mon, 03 Jun 2019 22:05:22: 4000000 INFO @ Mon, 03 Jun 2019 22:05:25: 5000000 INFO @ Mon, 03 Jun 2019 22:05:26: 5000000 INFO @ Mon, 03 Jun 2019 22:05:29: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:05:29: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:05:29: #1 total tags in treatment: 5598395 INFO @ Mon, 03 Jun 2019 22:05:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:05:29: #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 22:05:29: #1 tags after filtering in treatment: 5598395 INFO @ Mon, 03 Jun 2019 22:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:05:29: #1 finished! INFO @ Mon, 03 Jun 2019 22:05:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:05:30: #2 number of paired peaks: 428 WARNING @ Mon, 03 Jun 2019 22:05:30: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Mon, 03 Jun 2019 22:05:30: start model_add_line... INFO @ Mon, 03 Jun 2019 22:05:30: start X-correlation... INFO @ Mon, 03 Jun 2019 22:05:30: 5000000 INFO @ Mon, 03 Jun 2019 22:05:30: end of X-cor INFO @ Mon, 03 Jun 2019 22:05:30: #2 finished! INFO @ Mon, 03 Jun 2019 22:05:30: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 22:05:30: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 22:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.05_model.r WARNING @ Mon, 03 Jun 2019 22:05:30: #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 22:05:30: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 22:05:30: #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 22:05:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:05:30: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:05:30: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:05:30: #1 total tags in treatment: 5598395 INFO @ Mon, 03 Jun 2019 22:05:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:05:30: #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 22:05:30: #1 tags after filtering in treatment: 5598395 INFO @ Mon, 03 Jun 2019 22:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:05:30: #1 finished! INFO @ Mon, 03 Jun 2019 22:05:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:05:31: #2 number of paired peaks: 428 WARNING @ Mon, 03 Jun 2019 22:05:31: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Mon, 03 Jun 2019 22:05:31: start model_add_line... INFO @ Mon, 03 Jun 2019 22:05:31: start X-correlation... INFO @ Mon, 03 Jun 2019 22:05:31: end of X-cor INFO @ Mon, 03 Jun 2019 22:05:31: #2 finished! INFO @ Mon, 03 Jun 2019 22:05:31: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 22:05:31: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 22:05:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.10_model.r WARNING @ Mon, 03 Jun 2019 22:05:31: #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 22:05:31: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 22:05:31: #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 22:05:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:05:35: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:05:35: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:05:35: #1 total tags in treatment: 5598395 INFO @ Mon, 03 Jun 2019 22:05:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:05:35: #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 22:05:35: #1 tags after filtering in treatment: 5598395 INFO @ Mon, 03 Jun 2019 22:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:05:35: #1 finished! INFO @ Mon, 03 Jun 2019 22:05:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:05:35: #2 number of paired peaks: 428 WARNING @ Mon, 03 Jun 2019 22:05:35: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Mon, 03 Jun 2019 22:05:35: start model_add_line... INFO @ Mon, 03 Jun 2019 22:05:35: start X-correlation... INFO @ Mon, 03 Jun 2019 22:05:35: end of X-cor INFO @ Mon, 03 Jun 2019 22:05:35: #2 finished! INFO @ Mon, 03 Jun 2019 22:05:35: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 22:05:35: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 22:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.20_model.r WARNING @ Mon, 03 Jun 2019 22:05:35: #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 22:05:35: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 22:05:35: #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 22:05:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:05:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:05:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:05:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:05:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:05:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:05:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.05_summits.bed INFO @ Mon, 03 Jun 2019 22:05:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1228 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:05:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:05:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:05:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.10_summits.bed INFO @ Mon, 03 Jun 2019 22:05:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (888 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507389/SRX507389.20_summits.bed INFO @ Mon, 03 Jun 2019 22:06:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。