Job ID = 1300075 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T09:52:56 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 ) 2019-06-03T09:52:56 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 ) 2019-06-03T09:57:49 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 : 18,371,422 reads read : 18,371,422 reads written : 18,371,422 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: 00:09:03 18371422 reads; of these: 18371422 (100.00%) were unpaired; of these: 444956 (2.42%) aligned 0 times 12260980 (66.74%) aligned exactly 1 time 5665486 (30.84%) aligned >1 times 97.58% overall alignment rate Time searching: 00:09:03 Overall time: 00:09:03 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] 1688810 / 17926466 = 0.0942 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 19:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.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 19:13:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.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 19:13:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.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 19:13:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:43: 1000000 INFO @ Mon, 03 Jun 2019 19:13:43: 1000000 INFO @ Mon, 03 Jun 2019 19:13:45: 1000000 INFO @ Mon, 03 Jun 2019 19:13:54: 2000000 INFO @ Mon, 03 Jun 2019 19:13:54: 2000000 INFO @ Mon, 03 Jun 2019 19:13:56: 2000000 INFO @ Mon, 03 Jun 2019 19:14:04: 3000000 INFO @ Mon, 03 Jun 2019 19:14:04: 3000000 INFO @ Mon, 03 Jun 2019 19:14:09: 3000000 INFO @ Mon, 03 Jun 2019 19:14:14: 4000000 INFO @ Mon, 03 Jun 2019 19:14:14: 4000000 INFO @ Mon, 03 Jun 2019 19:14:21: 4000000 INFO @ Mon, 03 Jun 2019 19:14:24: 5000000 INFO @ Mon, 03 Jun 2019 19:14:24: 5000000 INFO @ Mon, 03 Jun 2019 19:14:33: 5000000 INFO @ Mon, 03 Jun 2019 19:14:34: 6000000 INFO @ Mon, 03 Jun 2019 19:14:34: 6000000 INFO @ Mon, 03 Jun 2019 19:14:44: 7000000 INFO @ Mon, 03 Jun 2019 19:14:44: 7000000 INFO @ Mon, 03 Jun 2019 19:14:45: 6000000 INFO @ Mon, 03 Jun 2019 19:14:54: 8000000 INFO @ Mon, 03 Jun 2019 19:14:54: 8000000 INFO @ Mon, 03 Jun 2019 19:14:56: 7000000 INFO @ Mon, 03 Jun 2019 19:15:03: 9000000 INFO @ Mon, 03 Jun 2019 19:15:03: 9000000 INFO @ Mon, 03 Jun 2019 19:15:09: 8000000 INFO @ Mon, 03 Jun 2019 19:15:12: 10000000 INFO @ Mon, 03 Jun 2019 19:15:13: 10000000 INFO @ Mon, 03 Jun 2019 19:15:21: 9000000 INFO @ Mon, 03 Jun 2019 19:15:22: 11000000 INFO @ Mon, 03 Jun 2019 19:15:22: 11000000 INFO @ Mon, 03 Jun 2019 19:15:32: 12000000 INFO @ Mon, 03 Jun 2019 19:15:32: 12000000 INFO @ Mon, 03 Jun 2019 19:15:32: 10000000 INFO @ Mon, 03 Jun 2019 19:15:41: 13000000 INFO @ Mon, 03 Jun 2019 19:15:41: 13000000 INFO @ Mon, 03 Jun 2019 19:15:44: 11000000 INFO @ Mon, 03 Jun 2019 19:15:50: 14000000 INFO @ Mon, 03 Jun 2019 19:15:50: 14000000 INFO @ Mon, 03 Jun 2019 19:15:55: 12000000 INFO @ Mon, 03 Jun 2019 19:15:59: 15000000 INFO @ Mon, 03 Jun 2019 19:16:00: 15000000 INFO @ Mon, 03 Jun 2019 19:16:06: 13000000 INFO @ Mon, 03 Jun 2019 19:16:09: 16000000 INFO @ Mon, 03 Jun 2019 19:16:09: 16000000 INFO @ Mon, 03 Jun 2019 19:16:11: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:16:11: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:16:11: #1 total tags in treatment: 16237656 INFO @ Mon, 03 Jun 2019 19:16:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:16:11: #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 19:16:11: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:16:11: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:16:11: #1 total tags in treatment: 16237656 INFO @ Mon, 03 Jun 2019 19:16:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:16:11: #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 19:16:11: #1 tags after filtering in treatment: 16237656 INFO @ Mon, 03 Jun 2019 19:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:16:11: #1 finished! INFO @ Mon, 03 Jun 2019 19:16:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:16:11: #1 tags after filtering in treatment: 16237656 INFO @ Mon, 03 Jun 2019 19:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:16:11: #1 finished! INFO @ Mon, 03 Jun 2019 19:16:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:16:13: #2 number of paired peaks: 922 WARNING @ Mon, 03 Jun 2019 19:16:13: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Mon, 03 Jun 2019 19:16:13: start model_add_line... INFO @ Mon, 03 Jun 2019 19:16:13: #2 number of paired peaks: 922 WARNING @ Mon, 03 Jun 2019 19:16:13: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Mon, 03 Jun 2019 19:16:13: start model_add_line... INFO @ Mon, 03 Jun 2019 19:16:13: start X-correlation... INFO @ Mon, 03 Jun 2019 19:16:13: end of X-cor INFO @ Mon, 03 Jun 2019 19:16:13: #2 finished! INFO @ Mon, 03 Jun 2019 19:16:13: #2 predicted fragment length is 162 bps INFO @ Mon, 03 Jun 2019 19:16:13: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 03 Jun 2019 19:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.20_model.r INFO @ Mon, 03 Jun 2019 19:16:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:16:13: start X-correlation... INFO @ Mon, 03 Jun 2019 19:16:13: end of X-cor INFO @ Mon, 03 Jun 2019 19:16:13: #2 finished! INFO @ Mon, 03 Jun 2019 19:16:13: #2 predicted fragment length is 162 bps INFO @ Mon, 03 Jun 2019 19:16:13: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 03 Jun 2019 19:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.05_model.r INFO @ Mon, 03 Jun 2019 19:16:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:16:18: 14000000 INFO @ Mon, 03 Jun 2019 19:16:29: 15000000 INFO @ Mon, 03 Jun 2019 19:16:40: 16000000 INFO @ Mon, 03 Jun 2019 19:16:43: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:16:43: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:16:43: #1 total tags in treatment: 16237656 INFO @ Mon, 03 Jun 2019 19:16:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:16:43: #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 19:16:43: #1 tags after filtering in treatment: 16237656 INFO @ Mon, 03 Jun 2019 19:16:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:16:43: #1 finished! INFO @ Mon, 03 Jun 2019 19:16:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:16:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:16:45: #2 number of paired peaks: 922 WARNING @ Mon, 03 Jun 2019 19:16:45: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Mon, 03 Jun 2019 19:16:45: start model_add_line... INFO @ Mon, 03 Jun 2019 19:16:45: start X-correlation... INFO @ Mon, 03 Jun 2019 19:16:45: end of X-cor INFO @ Mon, 03 Jun 2019 19:16:45: #2 finished! INFO @ Mon, 03 Jun 2019 19:16:45: #2 predicted fragment length is 162 bps INFO @ Mon, 03 Jun 2019 19:16:45: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 03 Jun 2019 19:16:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.10_model.r INFO @ Mon, 03 Jun 2019 19:16:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:16:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:16:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.20_summits.bed INFO @ Mon, 03 Jun 2019 19:17:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1627 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.05_summits.bed INFO @ Mon, 03 Jun 2019 19:17:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4259 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:17:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:17:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:17:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:17:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801806/SRX4801806.10_summits.bed INFO @ Mon, 03 Jun 2019 19:17:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2701 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。