Job ID = 1294506 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:30:17 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 ) 2019-06-02T23:30:17 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 ) 2019-06-02T23:33:28 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 : 13,702,188 reads read : 13,702,188 reads written : 13,702,188 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: 00:04:14 13702188 reads; of these: 13702188 (100.00%) were unpaired; of these: 672007 (4.90%) aligned 0 times 11255705 (82.15%) aligned exactly 1 time 1774476 (12.95%) aligned >1 times 95.10% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 1212906 / 13030181 = 0.0931 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 08:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.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 08:45:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:45:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.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 08:45:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:45:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.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 08:45:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:45:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:45:30: 1000000 INFO @ Mon, 03 Jun 2019 08:45:32: 1000000 INFO @ Mon, 03 Jun 2019 08:45:33: 1000000 INFO @ Mon, 03 Jun 2019 08:45:38: 2000000 INFO @ Mon, 03 Jun 2019 08:45:40: 2000000 INFO @ Mon, 03 Jun 2019 08:45:42: 2000000 INFO @ Mon, 03 Jun 2019 08:45:45: 3000000 INFO @ Mon, 03 Jun 2019 08:45:48: 3000000 INFO @ Mon, 03 Jun 2019 08:45:51: 3000000 INFO @ Mon, 03 Jun 2019 08:45:53: 4000000 INFO @ Mon, 03 Jun 2019 08:45:56: 4000000 INFO @ Mon, 03 Jun 2019 08:46:00: 5000000 INFO @ Mon, 03 Jun 2019 08:46:01: 4000000 INFO @ Mon, 03 Jun 2019 08:46:05: 5000000 INFO @ Mon, 03 Jun 2019 08:46:08: 6000000 INFO @ Mon, 03 Jun 2019 08:46:11: 5000000 INFO @ Mon, 03 Jun 2019 08:46:13: 6000000 INFO @ Mon, 03 Jun 2019 08:46:15: 7000000 INFO @ Mon, 03 Jun 2019 08:46:20: 6000000 INFO @ Mon, 03 Jun 2019 08:46:22: 7000000 INFO @ Mon, 03 Jun 2019 08:46:23: 8000000 INFO @ Mon, 03 Jun 2019 08:46:30: 7000000 INFO @ Mon, 03 Jun 2019 08:46:30: 8000000 INFO @ Mon, 03 Jun 2019 08:46:30: 9000000 INFO @ Mon, 03 Jun 2019 08:46:38: 10000000 INFO @ Mon, 03 Jun 2019 08:46:39: 9000000 INFO @ Mon, 03 Jun 2019 08:46:39: 8000000 INFO @ Mon, 03 Jun 2019 08:46:46: 11000000 INFO @ Mon, 03 Jun 2019 08:46:48: 10000000 INFO @ Mon, 03 Jun 2019 08:46:49: 9000000 INFO @ Mon, 03 Jun 2019 08:46:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:46:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:46:52: #1 total tags in treatment: 11817275 INFO @ Mon, 03 Jun 2019 08:46:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:46:52: #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 08:46:52: #1 tags after filtering in treatment: 11817275 INFO @ Mon, 03 Jun 2019 08:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:46:52: #1 finished! INFO @ Mon, 03 Jun 2019 08:46:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:46:53: #2 number of paired peaks: 502 WARNING @ Mon, 03 Jun 2019 08:46:53: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 03 Jun 2019 08:46:53: start model_add_line... INFO @ Mon, 03 Jun 2019 08:46:54: start X-correlation... INFO @ Mon, 03 Jun 2019 08:46:54: end of X-cor INFO @ Mon, 03 Jun 2019 08:46:54: #2 finished! INFO @ Mon, 03 Jun 2019 08:46:54: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 08:46:54: #2 alternative fragment length(s) may be 3,102,124,139 bps INFO @ Mon, 03 Jun 2019 08:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.05_model.r INFO @ Mon, 03 Jun 2019 08:46:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:46:58: 11000000 INFO @ Mon, 03 Jun 2019 08:46:59: 10000000 INFO @ Mon, 03 Jun 2019 08:47:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:47:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:47:05: #1 total tags in treatment: 11817275 INFO @ Mon, 03 Jun 2019 08:47:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:47:05: #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 08:47:06: #1 tags after filtering in treatment: 11817275 INFO @ Mon, 03 Jun 2019 08:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:47:06: #1 finished! INFO @ Mon, 03 Jun 2019 08:47:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:47:07: #2 number of paired peaks: 502 WARNING @ Mon, 03 Jun 2019 08:47:07: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 03 Jun 2019 08:47:07: start model_add_line... INFO @ Mon, 03 Jun 2019 08:47:07: start X-correlation... INFO @ Mon, 03 Jun 2019 08:47:07: end of X-cor INFO @ Mon, 03 Jun 2019 08:47:07: #2 finished! INFO @ Mon, 03 Jun 2019 08:47:07: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 08:47:07: #2 alternative fragment length(s) may be 3,102,124,139 bps INFO @ Mon, 03 Jun 2019 08:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.10_model.r INFO @ Mon, 03 Jun 2019 08:47:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:47:09: 11000000 INFO @ Mon, 03 Jun 2019 08:47:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:47:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:47:16: #1 total tags in treatment: 11817275 INFO @ Mon, 03 Jun 2019 08:47:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:47:16: #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 08:47:17: #1 tags after filtering in treatment: 11817275 INFO @ Mon, 03 Jun 2019 08:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:47:17: #1 finished! INFO @ Mon, 03 Jun 2019 08:47:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:47:18: #2 number of paired peaks: 502 WARNING @ Mon, 03 Jun 2019 08:47:18: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 03 Jun 2019 08:47:18: start model_add_line... INFO @ Mon, 03 Jun 2019 08:47:18: start X-correlation... INFO @ Mon, 03 Jun 2019 08:47:18: end of X-cor INFO @ Mon, 03 Jun 2019 08:47:18: #2 finished! INFO @ Mon, 03 Jun 2019 08:47:18: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 08:47:18: #2 alternative fragment length(s) may be 3,102,124,139 bps INFO @ Mon, 03 Jun 2019 08:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.20_model.r INFO @ Mon, 03 Jun 2019 08:47:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:47:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.05_summits.bed INFO @ Mon, 03 Jun 2019 08:47:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2901 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:47:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.10_summits.bed INFO @ Mon, 03 Jun 2019 08:47:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1231 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287704/SRX287704.20_summits.bed INFO @ Mon, 03 Jun 2019 08:48:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (504 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。