Job ID = 1307630 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:26:16 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 ) 2019-06-03T13:26:16 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 : 16,167,549 reads read : 32,335,098 reads written : 16,167,549 reads 0-length : 16,167,549 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: 00:13:12 16167549 reads; of these: 16167549 (100.00%) were unpaired; of these: 1095653 (6.78%) aligned 0 times 5590582 (34.58%) aligned exactly 1 time 9481314 (58.64%) aligned >1 times 93.22% overall alignment rate Time searching: 00:13:12 Overall time: 00:13:12 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] 4646772 / 15071896 = 0.3083 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 22:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.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 22:47:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:47:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.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 22:47:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:47:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.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 22:47:35: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:47:35: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:47:44: 1000000 INFO @ Mon, 03 Jun 2019 22:47:45: 1000000 INFO @ Mon, 03 Jun 2019 22:47:45: 1000000 INFO @ Mon, 03 Jun 2019 22:47:55: 2000000 INFO @ Mon, 03 Jun 2019 22:47:56: 2000000 INFO @ Mon, 03 Jun 2019 22:47:56: 2000000 INFO @ Mon, 03 Jun 2019 22:48:04: 3000000 INFO @ Mon, 03 Jun 2019 22:48:06: 3000000 INFO @ Mon, 03 Jun 2019 22:48:06: 3000000 INFO @ Mon, 03 Jun 2019 22:48:13: 4000000 INFO @ Mon, 03 Jun 2019 22:48:16: 4000000 INFO @ Mon, 03 Jun 2019 22:48:16: 4000000 INFO @ Mon, 03 Jun 2019 22:48:22: 5000000 INFO @ Mon, 03 Jun 2019 22:48:26: 5000000 INFO @ Mon, 03 Jun 2019 22:48:27: 5000000 INFO @ Mon, 03 Jun 2019 22:48:32: 6000000 INFO @ Mon, 03 Jun 2019 22:48:37: 6000000 INFO @ Mon, 03 Jun 2019 22:48:38: 6000000 INFO @ Mon, 03 Jun 2019 22:48:43: 7000000 INFO @ Mon, 03 Jun 2019 22:48:48: 7000000 INFO @ Mon, 03 Jun 2019 22:48:49: 7000000 INFO @ Mon, 03 Jun 2019 22:48:55: 8000000 INFO @ Mon, 03 Jun 2019 22:48:59: 8000000 INFO @ Mon, 03 Jun 2019 22:49:00: 8000000 INFO @ Mon, 03 Jun 2019 22:49:07: 9000000 INFO @ Mon, 03 Jun 2019 22:49:10: 9000000 INFO @ Mon, 03 Jun 2019 22:49:11: 9000000 INFO @ Mon, 03 Jun 2019 22:49:19: 10000000 INFO @ Mon, 03 Jun 2019 22:49:21: 10000000 INFO @ Mon, 03 Jun 2019 22:49:22: 10000000 INFO @ Mon, 03 Jun 2019 22:49:24: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:49:24: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:49:24: #1 total tags in treatment: 10425124 INFO @ Mon, 03 Jun 2019 22:49:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:49:24: #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 22:49:24: #1 tags after filtering in treatment: 10425124 INFO @ Mon, 03 Jun 2019 22:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:49:24: #1 finished! INFO @ Mon, 03 Jun 2019 22:49:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:49:25: #2 number of paired peaks: 2136 INFO @ Mon, 03 Jun 2019 22:49:25: start model_add_line... INFO @ Mon, 03 Jun 2019 22:49:25: start X-correlation... INFO @ Mon, 03 Jun 2019 22:49:25: end of X-cor INFO @ Mon, 03 Jun 2019 22:49:25: #2 finished! INFO @ Mon, 03 Jun 2019 22:49:25: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 22:49:25: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 22:49:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.10_model.r WARNING @ Mon, 03 Jun 2019 22:49:25: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:49:25: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 22:49:25: #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 22:49:25: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:49:26: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:49:26: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:49:26: #1 total tags in treatment: 10425124 INFO @ Mon, 03 Jun 2019 22:49:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:49:26: #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 22:49:26: #1 tags after filtering in treatment: 10425124 INFO @ Mon, 03 Jun 2019 22:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:49:26: #1 finished! INFO @ Mon, 03 Jun 2019 22:49:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:49:27: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:49:27: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:49:27: #1 total tags in treatment: 10425124 INFO @ Mon, 03 Jun 2019 22:49:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:49:27: #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 22:49:27: #1 tags after filtering in treatment: 10425124 INFO @ Mon, 03 Jun 2019 22:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:49:27: #1 finished! INFO @ Mon, 03 Jun 2019 22:49:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:49:27: #2 number of paired peaks: 2136 INFO @ Mon, 03 Jun 2019 22:49:27: start model_add_line... INFO @ Mon, 03 Jun 2019 22:49:27: start X-correlation... INFO @ Mon, 03 Jun 2019 22:49:27: end of X-cor INFO @ Mon, 03 Jun 2019 22:49:27: #2 finished! INFO @ Mon, 03 Jun 2019 22:49:27: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 22:49:27: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 22:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.20_model.r WARNING @ Mon, 03 Jun 2019 22:49:27: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:49:27: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 22:49:27: #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 22:49:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:49:28: #2 number of paired peaks: 2136 INFO @ Mon, 03 Jun 2019 22:49:28: start model_add_line... INFO @ Mon, 03 Jun 2019 22:49:28: start X-correlation... INFO @ Mon, 03 Jun 2019 22:49:28: end of X-cor INFO @ Mon, 03 Jun 2019 22:49:28: #2 finished! INFO @ Mon, 03 Jun 2019 22:49:28: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 22:49:28: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 22:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.05_model.r WARNING @ Mon, 03 Jun 2019 22:49:28: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:49:28: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 22:49:28: #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 22:49:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:49:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:49:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:49:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.20_summits.bed INFO @ Mon, 03 Jun 2019 22:50:13: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1306 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:50:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:50:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.05_summits.bed INFO @ Mon, 03 Jun 2019 22:50:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8200 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343101/SRX5343101.10_summits.bed INFO @ Mon, 03 Jun 2019 22:50:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3066 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。