Job ID = 1293666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:27:19 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 ) 2019-06-02T16:27:19 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( UNKNOWN ERROR CODE (004NET - Reading information from the socket failed ) 2019-06-02T16:27:19 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( UNKNOWN ERROR CODE (004NET - Reading information from the socket failed ) 2019-06-02T16:27:19 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 : 22,233,630 reads read : 22,233,630 reads written : 22,233,630 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: 00:05:55 22233630 reads; of these: 22233630 (100.00%) were unpaired; of these: 739936 (3.33%) aligned 0 times 16914154 (76.07%) aligned exactly 1 time 4579540 (20.60%) aligned >1 times 96.67% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 2953091 / 21493694 = 0.1374 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 01:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.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 01:43:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:43:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.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 01:43:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:43:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:43:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.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 01:43:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:43:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:43:40: 1000000 INFO @ Mon, 03 Jun 2019 01:43:41: 1000000 INFO @ Mon, 03 Jun 2019 01:43:41: 1000000 INFO @ Mon, 03 Jun 2019 01:43:49: 2000000 INFO @ Mon, 03 Jun 2019 01:43:50: 2000000 INFO @ Mon, 03 Jun 2019 01:43:52: 2000000 INFO @ Mon, 03 Jun 2019 01:43:57: 3000000 INFO @ Mon, 03 Jun 2019 01:44:00: 3000000 INFO @ Mon, 03 Jun 2019 01:44:02: 3000000 INFO @ Mon, 03 Jun 2019 01:44:05: 4000000 INFO @ Mon, 03 Jun 2019 01:44:09: 4000000 INFO @ Mon, 03 Jun 2019 01:44:12: 4000000 INFO @ Mon, 03 Jun 2019 01:44:15: 5000000 INFO @ Mon, 03 Jun 2019 01:44:18: 5000000 INFO @ Mon, 03 Jun 2019 01:44:22: 5000000 INFO @ Mon, 03 Jun 2019 01:44:23: 6000000 INFO @ Mon, 03 Jun 2019 01:44:28: 6000000 INFO @ Mon, 03 Jun 2019 01:44:31: 7000000 INFO @ Mon, 03 Jun 2019 01:44:32: 6000000 INFO @ Mon, 03 Jun 2019 01:44:38: 7000000 INFO @ Mon, 03 Jun 2019 01:44:39: 8000000 INFO @ Mon, 03 Jun 2019 01:44:42: 7000000 INFO @ Mon, 03 Jun 2019 01:44:47: 9000000 INFO @ Mon, 03 Jun 2019 01:44:47: 8000000 INFO @ Mon, 03 Jun 2019 01:44:52: 8000000 INFO @ Mon, 03 Jun 2019 01:44:54: 10000000 INFO @ Mon, 03 Jun 2019 01:44:56: 9000000 INFO @ Mon, 03 Jun 2019 01:45:02: 9000000 INFO @ Mon, 03 Jun 2019 01:45:02: 11000000 INFO @ Mon, 03 Jun 2019 01:45:06: 10000000 INFO @ Mon, 03 Jun 2019 01:45:10: 12000000 INFO @ Mon, 03 Jun 2019 01:45:12: 10000000 INFO @ Mon, 03 Jun 2019 01:45:15: 11000000 INFO @ Mon, 03 Jun 2019 01:45:18: 13000000 INFO @ Mon, 03 Jun 2019 01:45:22: 11000000 INFO @ Mon, 03 Jun 2019 01:45:24: 12000000 INFO @ Mon, 03 Jun 2019 01:45:26: 14000000 INFO @ Mon, 03 Jun 2019 01:45:32: 12000000 INFO @ Mon, 03 Jun 2019 01:45:33: 13000000 INFO @ Mon, 03 Jun 2019 01:45:34: 15000000 INFO @ Mon, 03 Jun 2019 01:45:41: 16000000 INFO @ Mon, 03 Jun 2019 01:45:42: 14000000 INFO @ Mon, 03 Jun 2019 01:45:43: 13000000 INFO @ Mon, 03 Jun 2019 01:45:49: 17000000 INFO @ Mon, 03 Jun 2019 01:45:52: 15000000 INFO @ Mon, 03 Jun 2019 01:45:53: 14000000 INFO @ Mon, 03 Jun 2019 01:45:58: 18000000 INFO @ Mon, 03 Jun 2019 01:46:02: 16000000 INFO @ Mon, 03 Jun 2019 01:46:02: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:46:02: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:46:02: #1 total tags in treatment: 18540603 INFO @ Mon, 03 Jun 2019 01:46:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:46:02: #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 01:46:03: #1 tags after filtering in treatment: 18540603 INFO @ Mon, 03 Jun 2019 01:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:46:03: #1 finished! INFO @ Mon, 03 Jun 2019 01:46:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:46:03: 15000000 INFO @ Mon, 03 Jun 2019 01:46:04: #2 number of paired peaks: 404 WARNING @ Mon, 03 Jun 2019 01:46:04: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Mon, 03 Jun 2019 01:46:04: start model_add_line... INFO @ Mon, 03 Jun 2019 01:46:05: start X-correlation... INFO @ Mon, 03 Jun 2019 01:46:05: end of X-cor INFO @ Mon, 03 Jun 2019 01:46:05: #2 finished! INFO @ Mon, 03 Jun 2019 01:46:05: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 01:46:05: #2 alternative fragment length(s) may be 4,136,140 bps INFO @ Mon, 03 Jun 2019 01:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.10_model.r INFO @ Mon, 03 Jun 2019 01:46:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:46:11: 17000000 INFO @ Mon, 03 Jun 2019 01:46:13: 16000000 INFO @ Mon, 03 Jun 2019 01:46:20: 18000000 INFO @ Mon, 03 Jun 2019 01:46:22: 17000000 INFO @ Mon, 03 Jun 2019 01:46:25: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:46:25: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:46:25: #1 total tags in treatment: 18540603 INFO @ Mon, 03 Jun 2019 01:46:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:46:25: #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 01:46:26: #1 tags after filtering in treatment: 18540603 INFO @ Mon, 03 Jun 2019 01:46:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:46:26: #1 finished! INFO @ Mon, 03 Jun 2019 01:46:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:46:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:46:28: #2 number of paired peaks: 404 WARNING @ Mon, 03 Jun 2019 01:46:28: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Mon, 03 Jun 2019 01:46:28: start model_add_line... INFO @ Mon, 03 Jun 2019 01:46:28: start X-correlation... INFO @ Mon, 03 Jun 2019 01:46:28: end of X-cor INFO @ Mon, 03 Jun 2019 01:46:28: #2 finished! INFO @ Mon, 03 Jun 2019 01:46:28: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 01:46:28: #2 alternative fragment length(s) may be 4,136,140 bps INFO @ Mon, 03 Jun 2019 01:46:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.05_model.r INFO @ Mon, 03 Jun 2019 01:46:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:46:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:46:32: 18000000 INFO @ Mon, 03 Jun 2019 01:46:37: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 01:46:37: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 01:46:37: #1 total tags in treatment: 18540603 INFO @ Mon, 03 Jun 2019 01:46:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:46:37: #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 01:46:37: #1 tags after filtering in treatment: 18540603 INFO @ Mon, 03 Jun 2019 01:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:46:37: #1 finished! INFO @ Mon, 03 Jun 2019 01:46:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:46:39: #2 number of paired peaks: 404 WARNING @ Mon, 03 Jun 2019 01:46:39: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Mon, 03 Jun 2019 01:46:39: start model_add_line... INFO @ Mon, 03 Jun 2019 01:46:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:46:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:46:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:46:39: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 01:46:39: #2 alternative fragment length(s) may be 4,136,140 bps INFO @ Mon, 03 Jun 2019 01:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.20_model.r INFO @ Mon, 03 Jun 2019 01:46:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:47:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.10_summits.bed INFO @ Mon, 03 Jun 2019 01:47:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (960 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:47:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.05_summits.bed INFO @ Mon, 03 Jun 2019 01:47:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3901 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104978/SRX104978.20_summits.bed INFO @ Mon, 03 Jun 2019 01:47:58: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。