Job ID = 1293648 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:24:45 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 : 38,991,196 reads read : 38,991,196 reads written : 38,991,196 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:25 38991196 reads; of these: 38991196 (100.00%) were unpaired; of these: 2599083 (6.67%) aligned 0 times 32544106 (83.47%) aligned exactly 1 time 3848007 (9.87%) aligned >1 times 93.33% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 11116283 / 36392113 = 0.3055 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 01:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.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 01:49:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:49:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.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 01:49:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:49:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.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 01:49:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:49:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:49:11: 1000000 INFO @ Mon, 03 Jun 2019 01:49:12: 1000000 INFO @ Mon, 03 Jun 2019 01:49:12: 1000000 INFO @ Mon, 03 Jun 2019 01:49:19: 2000000 INFO @ Mon, 03 Jun 2019 01:49:20: 2000000 INFO @ Mon, 03 Jun 2019 01:49:21: 2000000 INFO @ Mon, 03 Jun 2019 01:49:27: 3000000 INFO @ Mon, 03 Jun 2019 01:49:28: 3000000 INFO @ Mon, 03 Jun 2019 01:49:30: 3000000 INFO @ Mon, 03 Jun 2019 01:49:35: 4000000 INFO @ Mon, 03 Jun 2019 01:49:36: 4000000 INFO @ Mon, 03 Jun 2019 01:49:38: 4000000 INFO @ Mon, 03 Jun 2019 01:49:43: 5000000 INFO @ Mon, 03 Jun 2019 01:49:43: 5000000 INFO @ Mon, 03 Jun 2019 01:49:47: 5000000 INFO @ Mon, 03 Jun 2019 01:49:51: 6000000 INFO @ Mon, 03 Jun 2019 01:49:51: 6000000 INFO @ Mon, 03 Jun 2019 01:49:56: 6000000 INFO @ Mon, 03 Jun 2019 01:49:59: 7000000 INFO @ Mon, 03 Jun 2019 01:49:59: 7000000 INFO @ Mon, 03 Jun 2019 01:50:04: 7000000 INFO @ Mon, 03 Jun 2019 01:50:07: 8000000 INFO @ Mon, 03 Jun 2019 01:50:07: 8000000 INFO @ Mon, 03 Jun 2019 01:50:12: 8000000 INFO @ Mon, 03 Jun 2019 01:50:15: 9000000 INFO @ Mon, 03 Jun 2019 01:50:15: 9000000 INFO @ Mon, 03 Jun 2019 01:50:20: 9000000 INFO @ Mon, 03 Jun 2019 01:50:22: 10000000 INFO @ Mon, 03 Jun 2019 01:50:23: 10000000 INFO @ Mon, 03 Jun 2019 01:50:28: 10000000 INFO @ Mon, 03 Jun 2019 01:50:30: 11000000 INFO @ Mon, 03 Jun 2019 01:50:31: 11000000 INFO @ Mon, 03 Jun 2019 01:50:35: 11000000 INFO @ Mon, 03 Jun 2019 01:50:38: 12000000 INFO @ Mon, 03 Jun 2019 01:50:38: 12000000 INFO @ Mon, 03 Jun 2019 01:50:43: 12000000 INFO @ Mon, 03 Jun 2019 01:50:46: 13000000 INFO @ Mon, 03 Jun 2019 01:50:46: 13000000 INFO @ Mon, 03 Jun 2019 01:50:50: 13000000 INFO @ Mon, 03 Jun 2019 01:50:53: 14000000 INFO @ Mon, 03 Jun 2019 01:50:54: 14000000 INFO @ Mon, 03 Jun 2019 01:50:58: 14000000 INFO @ Mon, 03 Jun 2019 01:51:01: 15000000 INFO @ Mon, 03 Jun 2019 01:51:01: 15000000 INFO @ Mon, 03 Jun 2019 01:51:06: 15000000 INFO @ Mon, 03 Jun 2019 01:51:09: 16000000 INFO @ Mon, 03 Jun 2019 01:51:09: 16000000 INFO @ Mon, 03 Jun 2019 01:51:13: 16000000 INFO @ Mon, 03 Jun 2019 01:51:16: 17000000 INFO @ Mon, 03 Jun 2019 01:51:17: 17000000 INFO @ Mon, 03 Jun 2019 01:51:21: 17000000 INFO @ Mon, 03 Jun 2019 01:51:24: 18000000 INFO @ Mon, 03 Jun 2019 01:51:24: 18000000 INFO @ Mon, 03 Jun 2019 01:51:29: 18000000 INFO @ Mon, 03 Jun 2019 01:51:32: 19000000 INFO @ Mon, 03 Jun 2019 01:51:32: 19000000 INFO @ Mon, 03 Jun 2019 01:51:36: 19000000 INFO @ Mon, 03 Jun 2019 01:51:39: 20000000 INFO @ Mon, 03 Jun 2019 01:51:40: 20000000 INFO @ Mon, 03 Jun 2019 01:51:44: 20000000 INFO @ Mon, 03 Jun 2019 01:51:47: 21000000 INFO @ Mon, 03 Jun 2019 01:51:47: 21000000 INFO @ Mon, 03 Jun 2019 01:51:51: 21000000 INFO @ Mon, 03 Jun 2019 01:51:55: 22000000 INFO @ Mon, 03 Jun 2019 01:51:56: 22000000 INFO @ Mon, 03 Jun 2019 01:51:59: 22000000 INFO @ Mon, 03 Jun 2019 01:52:02: 23000000 INFO @ Mon, 03 Jun 2019 01:52:04: 23000000 INFO @ Mon, 03 Jun 2019 01:52:07: 23000000 INFO @ Mon, 03 Jun 2019 01:52:10: 24000000 INFO @ Mon, 03 Jun 2019 01:52:12: 24000000 INFO @ Mon, 03 Jun 2019 01:52:14: 24000000 INFO @ Mon, 03 Jun 2019 01:52:17: 25000000 INFO @ Mon, 03 Jun 2019 01:52:19: 25000000 INFO @ Mon, 03 Jun 2019 01:52:20: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:52:20: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:52:20: #1 total tags in treatment: 25275830 INFO @ Mon, 03 Jun 2019 01:52:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:52:20: #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 01:52:20: #1 tags after filtering in treatment: 25275830 INFO @ Mon, 03 Jun 2019 01:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:52:20: #1 finished! INFO @ Mon, 03 Jun 2019 01:52:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:52:21: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:52:21: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:52:21: #1 total tags in treatment: 25275830 INFO @ Mon, 03 Jun 2019 01:52:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:52:21: #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 01:52:22: #1 tags after filtering in treatment: 25275830 INFO @ Mon, 03 Jun 2019 01:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:52:22: #1 finished! INFO @ Mon, 03 Jun 2019 01:52:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:52:22: 25000000 INFO @ Mon, 03 Jun 2019 01:52:22: #2 number of paired peaks: 441 WARNING @ Mon, 03 Jun 2019 01:52:22: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Mon, 03 Jun 2019 01:52:22: start model_add_line... INFO @ Mon, 03 Jun 2019 01:52:23: start X-correlation... INFO @ Mon, 03 Jun 2019 01:52:23: end of X-cor INFO @ Mon, 03 Jun 2019 01:52:23: #2 finished! INFO @ Mon, 03 Jun 2019 01:52:23: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 01:52:23: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 01:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.10_model.r INFO @ Mon, 03 Jun 2019 01:52:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:52:24: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:52:24: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:52:24: #1 total tags in treatment: 25275830 INFO @ Mon, 03 Jun 2019 01:52:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:52:24: #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 01:52:24: #2 number of paired peaks: 441 WARNING @ Mon, 03 Jun 2019 01:52:24: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Mon, 03 Jun 2019 01:52:24: start model_add_line... INFO @ Mon, 03 Jun 2019 01:52:24: start X-correlation... INFO @ Mon, 03 Jun 2019 01:52:24: end of X-cor INFO @ Mon, 03 Jun 2019 01:52:24: #2 finished! INFO @ Mon, 03 Jun 2019 01:52:24: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 01:52:24: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 01:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.05_model.r INFO @ Mon, 03 Jun 2019 01:52:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:52:25: #1 tags after filtering in treatment: 25275830 INFO @ Mon, 03 Jun 2019 01:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:52:25: #1 finished! INFO @ Mon, 03 Jun 2019 01:52:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:52:27: #2 number of paired peaks: 441 WARNING @ Mon, 03 Jun 2019 01:52:27: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Mon, 03 Jun 2019 01:52:27: start model_add_line... INFO @ Mon, 03 Jun 2019 01:52:27: start X-correlation... INFO @ Mon, 03 Jun 2019 01:52:27: end of X-cor INFO @ Mon, 03 Jun 2019 01:52:27: #2 finished! INFO @ Mon, 03 Jun 2019 01:52:27: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 01:52:27: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 01:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.20_model.r INFO @ Mon, 03 Jun 2019 01:52:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:53:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:53:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:53:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.10_summits.bed INFO @ Mon, 03 Jun 2019 01:53:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7779 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.05_summits.bed INFO @ Mon, 03 Jun 2019 01:54:01: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11397 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104962/SRX104962.20_summits.bed INFO @ Mon, 03 Jun 2019 01:54:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4859 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。