Job ID = 1301272 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:45:35 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 ) 2019-06-03T10:45:35 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 : 15,318,328 reads read : 15,318,328 reads written : 15,318,328 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: 00:03:55 15318328 reads; of these: 15318328 (100.00%) were unpaired; of these: 1281095 (8.36%) aligned 0 times 11888978 (77.61%) aligned exactly 1 time 2148255 (14.02%) aligned >1 times 91.64% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 3929188 / 14037233 = 0.2799 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 19:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.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 19:58:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:58:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.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 19:58:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:58:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.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 19:58:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:58:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:58:47: 1000000 INFO @ Mon, 03 Jun 2019 19:58:49: 1000000 INFO @ Mon, 03 Jun 2019 19:58:50: 1000000 INFO @ Mon, 03 Jun 2019 19:58:55: 2000000 INFO @ Mon, 03 Jun 2019 19:58:59: 2000000 INFO @ Mon, 03 Jun 2019 19:59:00: 2000000 INFO @ Mon, 03 Jun 2019 19:59:02: 3000000 INFO @ Mon, 03 Jun 2019 19:59:09: 3000000 INFO @ Mon, 03 Jun 2019 19:59:10: 4000000 INFO @ Mon, 03 Jun 2019 19:59:10: 3000000 INFO @ Mon, 03 Jun 2019 19:59:17: 5000000 INFO @ Mon, 03 Jun 2019 19:59:19: 4000000 INFO @ Mon, 03 Jun 2019 19:59:20: 4000000 INFO @ Mon, 03 Jun 2019 19:59:25: 6000000 INFO @ Mon, 03 Jun 2019 19:59:29: 5000000 INFO @ Mon, 03 Jun 2019 19:59:31: 5000000 INFO @ Mon, 03 Jun 2019 19:59:33: 7000000 INFO @ Mon, 03 Jun 2019 19:59:39: 6000000 INFO @ Mon, 03 Jun 2019 19:59:42: 8000000 INFO @ Mon, 03 Jun 2019 19:59:42: 6000000 INFO @ Mon, 03 Jun 2019 19:59:49: 7000000 INFO @ Mon, 03 Jun 2019 19:59:49: 9000000 INFO @ Mon, 03 Jun 2019 19:59:52: 7000000 INFO @ Mon, 03 Jun 2019 19:59:57: 10000000 INFO @ Mon, 03 Jun 2019 19:59:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:59:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:59:58: #1 total tags in treatment: 10108045 INFO @ Mon, 03 Jun 2019 19:59:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:59:58: #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 19:59:58: #1 tags after filtering in treatment: 10108045 INFO @ Mon, 03 Jun 2019 19:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:59:58: #1 finished! INFO @ Mon, 03 Jun 2019 19:59:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:59:59: #2 number of paired peaks: 307 WARNING @ Mon, 03 Jun 2019 19:59:59: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Mon, 03 Jun 2019 19:59:59: start model_add_line... INFO @ Mon, 03 Jun 2019 19:59:59: start X-correlation... INFO @ Mon, 03 Jun 2019 19:59:59: end of X-cor INFO @ Mon, 03 Jun 2019 19:59:59: #2 finished! INFO @ Mon, 03 Jun 2019 19:59:59: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 19:59:59: #2 alternative fragment length(s) may be 194,198 bps INFO @ Mon, 03 Jun 2019 19:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.10_model.r INFO @ Mon, 03 Jun 2019 19:59:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:59:59: 8000000 INFO @ Mon, 03 Jun 2019 20:00:03: 8000000 INFO @ Mon, 03 Jun 2019 20:00:11: 9000000 INFO @ Mon, 03 Jun 2019 20:00:15: 9000000 INFO @ Mon, 03 Jun 2019 20:00:22: 10000000 INFO @ Mon, 03 Jun 2019 20:00:23: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:00:23: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:00:23: #1 total tags in treatment: 10108045 INFO @ Mon, 03 Jun 2019 20:00:23: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:00:23: #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 20:00:23: #1 tags after filtering in treatment: 10108045 INFO @ Mon, 03 Jun 2019 20:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:00:23: #1 finished! INFO @ Mon, 03 Jun 2019 20:00:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:00:24: #2 number of paired peaks: 307 WARNING @ Mon, 03 Jun 2019 20:00:24: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Mon, 03 Jun 2019 20:00:24: start model_add_line... INFO @ Mon, 03 Jun 2019 20:00:24: start X-correlation... INFO @ Mon, 03 Jun 2019 20:00:24: end of X-cor INFO @ Mon, 03 Jun 2019 20:00:24: #2 finished! INFO @ Mon, 03 Jun 2019 20:00:24: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 20:00:24: #2 alternative fragment length(s) may be 194,198 bps INFO @ Mon, 03 Jun 2019 20:00:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.20_model.r INFO @ Mon, 03 Jun 2019 20:00:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:00:26: 10000000 INFO @ Mon, 03 Jun 2019 20:00:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:00:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:00:27: #1 total tags in treatment: 10108045 INFO @ Mon, 03 Jun 2019 20:00:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:00:27: #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 20:00:27: #1 tags after filtering in treatment: 10108045 INFO @ Mon, 03 Jun 2019 20:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:00:27: #1 finished! INFO @ Mon, 03 Jun 2019 20:00:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:00:28: #2 number of paired peaks: 307 WARNING @ Mon, 03 Jun 2019 20:00:28: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Mon, 03 Jun 2019 20:00:28: start model_add_line... INFO @ Mon, 03 Jun 2019 20:00:28: start X-correlation... INFO @ Mon, 03 Jun 2019 20:00:28: end of X-cor INFO @ Mon, 03 Jun 2019 20:00:28: #2 finished! INFO @ Mon, 03 Jun 2019 20:00:28: #2 predicted fragment length is 198 bps INFO @ Mon, 03 Jun 2019 20:00:28: #2 alternative fragment length(s) may be 194,198 bps INFO @ Mon, 03 Jun 2019 20:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.05_model.r INFO @ Mon, 03 Jun 2019 20:00:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:00:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.10_summits.bed INFO @ Mon, 03 Jun 2019 20:00:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:00:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:00:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:01:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:01:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:01:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.20_summits.bed INFO @ Mon, 03 Jun 2019 20:01:09: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485209/SRX485209.05_summits.bed INFO @ Mon, 03 Jun 2019 20:01:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1456 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。