Job ID = 1294563 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:55:16 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 ) 2019-06-02T23:58:36 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 ) 2019-06-02T23:58:36 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 ) 2019-06-02T23:58:36 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 : 24,586,327 reads read : 24,586,327 reads written : 24,586,327 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: 00:09:06 24586327 reads; of these: 24586327 (100.00%) were unpaired; of these: 1901645 (7.73%) aligned 0 times 17223070 (70.05%) aligned exactly 1 time 5461612 (22.21%) aligned >1 times 92.27% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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 12 files... [bam_rmdupse_core] 5466037 / 22684682 = 0.2410 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 09:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.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 09:22:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:22:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.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 09:22:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:22:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.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 09:22:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:22:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:23:06: 1000000 INFO @ Mon, 03 Jun 2019 09:23:07: 1000000 INFO @ Mon, 03 Jun 2019 09:23:08: 1000000 INFO @ Mon, 03 Jun 2019 09:23:14: 2000000 INFO @ Mon, 03 Jun 2019 09:23:15: 2000000 INFO @ Mon, 03 Jun 2019 09:23:17: 2000000 INFO @ Mon, 03 Jun 2019 09:23:23: 3000000 INFO @ Mon, 03 Jun 2019 09:23:24: 3000000 INFO @ Mon, 03 Jun 2019 09:23:26: 3000000 INFO @ Mon, 03 Jun 2019 09:23:32: 4000000 INFO @ Mon, 03 Jun 2019 09:23:33: 4000000 INFO @ Mon, 03 Jun 2019 09:23:35: 4000000 INFO @ Mon, 03 Jun 2019 09:23:41: 5000000 INFO @ Mon, 03 Jun 2019 09:23:42: 5000000 INFO @ Mon, 03 Jun 2019 09:23:44: 5000000 INFO @ Mon, 03 Jun 2019 09:23:50: 6000000 INFO @ Mon, 03 Jun 2019 09:23:51: 6000000 INFO @ Mon, 03 Jun 2019 09:23:53: 6000000 INFO @ Mon, 03 Jun 2019 09:23:59: 7000000 INFO @ Mon, 03 Jun 2019 09:24:00: 7000000 INFO @ Mon, 03 Jun 2019 09:24:02: 7000000 INFO @ Mon, 03 Jun 2019 09:24:08: 8000000 INFO @ Mon, 03 Jun 2019 09:24:09: 8000000 INFO @ Mon, 03 Jun 2019 09:24:10: 8000000 INFO @ Mon, 03 Jun 2019 09:24:17: 9000000 INFO @ Mon, 03 Jun 2019 09:24:17: 9000000 INFO @ Mon, 03 Jun 2019 09:24:19: 9000000 INFO @ Mon, 03 Jun 2019 09:24:25: 10000000 INFO @ Mon, 03 Jun 2019 09:24:25: 10000000 INFO @ Mon, 03 Jun 2019 09:24:27: 10000000 INFO @ Mon, 03 Jun 2019 09:24:33: 11000000 INFO @ Mon, 03 Jun 2019 09:24:34: 11000000 INFO @ Mon, 03 Jun 2019 09:24:36: 11000000 INFO @ Mon, 03 Jun 2019 09:24:42: 12000000 INFO @ Mon, 03 Jun 2019 09:24:42: 12000000 INFO @ Mon, 03 Jun 2019 09:24:45: 12000000 INFO @ Mon, 03 Jun 2019 09:24:50: 13000000 INFO @ Mon, 03 Jun 2019 09:24:51: 13000000 INFO @ Mon, 03 Jun 2019 09:24:55: 13000000 INFO @ Mon, 03 Jun 2019 09:24:59: 14000000 INFO @ Mon, 03 Jun 2019 09:24:59: 14000000 INFO @ Mon, 03 Jun 2019 09:25:05: 14000000 INFO @ Mon, 03 Jun 2019 09:25:07: 15000000 INFO @ Mon, 03 Jun 2019 09:25:08: 15000000 INFO @ Mon, 03 Jun 2019 09:25:15: 16000000 INFO @ Mon, 03 Jun 2019 09:25:16: 15000000 INFO @ Mon, 03 Jun 2019 09:25:17: 16000000 INFO @ Mon, 03 Jun 2019 09:25:23: 17000000 INFO @ Mon, 03 Jun 2019 09:25:25: 17000000 INFO @ Mon, 03 Jun 2019 09:25:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:25: #1 total tags in treatment: 17218645 INFO @ Mon, 03 Jun 2019 09:25:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:25: #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 09:25:26: #1 tags after filtering in treatment: 17218645 INFO @ Mon, 03 Jun 2019 09:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:26: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:27: 16000000 INFO @ Mon, 03 Jun 2019 09:25:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:27: #1 total tags in treatment: 17218645 INFO @ Mon, 03 Jun 2019 09:25:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:27: #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 09:25:27: #2 number of paired peaks: 667 WARNING @ Mon, 03 Jun 2019 09:25:27: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:27: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:27: #1 tags after filtering in treatment: 17218645 INFO @ Mon, 03 Jun 2019 09:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:27: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:27: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:27: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:27: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:27: #2 predicted fragment length is 240 bps INFO @ Mon, 03 Jun 2019 09:25:27: #2 alternative fragment length(s) may be 240 bps INFO @ Mon, 03 Jun 2019 09:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.20_model.r INFO @ Mon, 03 Jun 2019 09:25:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:29: #2 number of paired peaks: 667 WARNING @ Mon, 03 Jun 2019 09:25:29: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:29: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:29: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:29: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:29: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:29: #2 predicted fragment length is 240 bps INFO @ Mon, 03 Jun 2019 09:25:29: #2 alternative fragment length(s) may be 240 bps INFO @ Mon, 03 Jun 2019 09:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.05_model.r INFO @ Mon, 03 Jun 2019 09:25:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:36: 17000000 INFO @ Mon, 03 Jun 2019 09:25:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:39: #1 total tags in treatment: 17218645 INFO @ Mon, 03 Jun 2019 09:25:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:39: #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 09:25:39: #1 tags after filtering in treatment: 17218645 INFO @ Mon, 03 Jun 2019 09:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:39: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:40: #2 number of paired peaks: 667 WARNING @ Mon, 03 Jun 2019 09:25:40: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:40: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:41: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:41: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:41: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:41: #2 predicted fragment length is 240 bps INFO @ Mon, 03 Jun 2019 09:25:41: #2 alternative fragment length(s) may be 240 bps INFO @ Mon, 03 Jun 2019 09:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.10_model.r INFO @ Mon, 03 Jun 2019 09:25:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:26:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:26:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:26:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:26:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.20_summits.bed INFO @ Mon, 03 Jun 2019 09:26:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1615 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.05_summits.bed INFO @ Mon, 03 Jun 2019 09:26:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3017 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:26:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287743/SRX287743.10_summits.bed INFO @ Mon, 03 Jun 2019 09:26:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2200 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。