Job ID = 4178517 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:38:53 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 ) 2019-12-05T03:38:53 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 : 16,143,653 reads read : 16,143,653 reads written : 16,143,653 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:25 16143653 reads; of these: 16143653 (100.00%) were unpaired; of these: 1782513 (11.04%) aligned 0 times 9954911 (61.66%) aligned exactly 1 time 4406229 (27.29%) aligned >1 times 88.96% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 2728482 / 14361140 = 0.1900 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.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 @ Thu, 05 Dec 2019 12:53:38: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:53:38: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:53:54: 1000000 INFO @ Thu, 05 Dec 2019 12:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.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 @ Thu, 05 Dec 2019 12:54:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:54:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:54:17: 2000000 INFO @ Thu, 05 Dec 2019 12:54:28: 1000000 INFO @ Thu, 05 Dec 2019 12:54:32: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.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 @ Thu, 05 Dec 2019 12:54:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:54:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:54:45: 2000000 INFO @ Thu, 05 Dec 2019 12:54:48: 4000000 INFO @ Thu, 05 Dec 2019 12:54:54: 1000000 INFO @ Thu, 05 Dec 2019 12:54:57: 3000000 INFO @ Thu, 05 Dec 2019 12:55:00: 5000000 INFO @ Thu, 05 Dec 2019 12:55:06: 2000000 INFO @ Thu, 05 Dec 2019 12:55:06: 4000000 INFO @ Thu, 05 Dec 2019 12:55:13: 6000000 INFO @ Thu, 05 Dec 2019 12:55:17: 5000000 INFO @ Thu, 05 Dec 2019 12:55:18: 3000000 INFO @ Thu, 05 Dec 2019 12:55:25: 7000000 INFO @ Thu, 05 Dec 2019 12:55:27: 6000000 INFO @ Thu, 05 Dec 2019 12:55:30: 4000000 INFO @ Thu, 05 Dec 2019 12:55:37: 7000000 INFO @ Thu, 05 Dec 2019 12:55:38: 8000000 INFO @ Thu, 05 Dec 2019 12:55:42: 5000000 INFO @ Thu, 05 Dec 2019 12:55:48: 8000000 INFO @ Thu, 05 Dec 2019 12:55:51: 9000000 INFO @ Thu, 05 Dec 2019 12:55:55: 6000000 INFO @ Thu, 05 Dec 2019 12:55:58: 9000000 INFO @ Thu, 05 Dec 2019 12:56:05: 10000000 INFO @ Thu, 05 Dec 2019 12:56:07: 7000000 INFO @ Thu, 05 Dec 2019 12:56:08: 10000000 INFO @ Thu, 05 Dec 2019 12:56:18: 11000000 INFO @ Thu, 05 Dec 2019 12:56:19: 11000000 INFO @ Thu, 05 Dec 2019 12:56:19: 8000000 INFO @ Thu, 05 Dec 2019 12:56:25: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:56:25: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:56:25: #1 total tags in treatment: 11632658 INFO @ Thu, 05 Dec 2019 12:56:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:56:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:56:25: #1 tags after filtering in treatment: 11632658 INFO @ Thu, 05 Dec 2019 12:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:56:25: #1 finished! INFO @ Thu, 05 Dec 2019 12:56:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:56:26: #2 number of paired peaks: 183 WARNING @ Thu, 05 Dec 2019 12:56:26: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 05 Dec 2019 12:56:26: start model_add_line... INFO @ Thu, 05 Dec 2019 12:56:26: start X-correlation... INFO @ Thu, 05 Dec 2019 12:56:26: end of X-cor INFO @ Thu, 05 Dec 2019 12:56:26: #2 finished! INFO @ Thu, 05 Dec 2019 12:56:26: #2 predicted fragment length is 81 bps INFO @ Thu, 05 Dec 2019 12:56:26: #2 alternative fragment length(s) may be 54,81,509,536,598 bps INFO @ Thu, 05 Dec 2019 12:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.10_model.r WARNING @ Thu, 05 Dec 2019 12:56:26: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:56:26: #2 You may need to consider one of the other alternative d(s): 54,81,509,536,598 WARNING @ Thu, 05 Dec 2019 12:56:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:56:26: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:56:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:56:27: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:56:27: #1 total tags in treatment: 11632658 INFO @ Thu, 05 Dec 2019 12:56:27: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:56:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:56:27: #1 tags after filtering in treatment: 11632658 INFO @ Thu, 05 Dec 2019 12:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:56:27: #1 finished! INFO @ Thu, 05 Dec 2019 12:56:27: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:56:29: #2 number of paired peaks: 183 WARNING @ Thu, 05 Dec 2019 12:56:29: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 05 Dec 2019 12:56:29: start model_add_line... INFO @ Thu, 05 Dec 2019 12:56:29: start X-correlation... INFO @ Thu, 05 Dec 2019 12:56:29: end of X-cor INFO @ Thu, 05 Dec 2019 12:56:29: #2 finished! INFO @ Thu, 05 Dec 2019 12:56:29: #2 predicted fragment length is 81 bps INFO @ Thu, 05 Dec 2019 12:56:29: #2 alternative fragment length(s) may be 54,81,509,536,598 bps INFO @ Thu, 05 Dec 2019 12:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.05_model.r WARNING @ Thu, 05 Dec 2019 12:56:29: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:56:29: #2 You may need to consider one of the other alternative d(s): 54,81,509,536,598 WARNING @ Thu, 05 Dec 2019 12:56:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:56:29: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:56:32: 9000000 INFO @ Thu, 05 Dec 2019 12:56:44: 10000000 INFO @ Thu, 05 Dec 2019 12:56:55: 11000000 INFO @ Thu, 05 Dec 2019 12:57:00: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:57:03: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:57:03: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:57:03: #1 total tags in treatment: 11632658 INFO @ Thu, 05 Dec 2019 12:57:03: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:57:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:57:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:57:04: #1 tags after filtering in treatment: 11632658 INFO @ Thu, 05 Dec 2019 12:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:57:04: #1 finished! INFO @ Thu, 05 Dec 2019 12:57:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:57:05: #2 number of paired peaks: 183 WARNING @ Thu, 05 Dec 2019 12:57:05: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Thu, 05 Dec 2019 12:57:05: start model_add_line... INFO @ Thu, 05 Dec 2019 12:57:05: start X-correlation... INFO @ Thu, 05 Dec 2019 12:57:05: end of X-cor INFO @ Thu, 05 Dec 2019 12:57:05: #2 finished! INFO @ Thu, 05 Dec 2019 12:57:05: #2 predicted fragment length is 81 bps INFO @ Thu, 05 Dec 2019 12:57:05: #2 alternative fragment length(s) may be 54,81,509,536,598 bps INFO @ Thu, 05 Dec 2019 12:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.20_model.r WARNING @ Thu, 05 Dec 2019 12:57:05: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 12:57:05: #2 You may need to consider one of the other alternative d(s): 54,81,509,536,598 WARNING @ Thu, 05 Dec 2019 12:57:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 12:57:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:57:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.10_summits.bed INFO @ Thu, 05 Dec 2019 12:57:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (954 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.05_summits.bed INFO @ Thu, 05 Dec 2019 12:57:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1968 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:57:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:57:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:57:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:57:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717039/SRX5717039.20_summits.bed INFO @ Thu, 05 Dec 2019 12:57:56: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (213 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。