Job ID = 1294828 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:15:22 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T01:15:22 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra11/SRR/000849/SRR870116' 2019-06-03T01:15:31 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870116' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T01:15:31 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T01:27:08 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 ) 2019-06-03T01:27:08 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 : 20,798,631 reads read : 20,798,631 reads written : 20,798,631 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: 00:09:14 20798631 reads; of these: 20798631 (100.00%) were unpaired; of these: 1061109 (5.10%) aligned 0 times 13628146 (65.52%) aligned exactly 1 time 6109376 (29.37%) aligned >1 times 94.90% overall alignment rate Time searching: 00:09:14 Overall time: 00:09:14 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 12 files... [bam_rmdupse_core] 3258667 / 19737522 = 0.1651 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 10:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.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 10:52:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.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 10:52:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.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 10:52:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:52:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:52:53: 1000000 INFO @ Mon, 03 Jun 2019 10:52:53: 1000000 INFO @ Mon, 03 Jun 2019 10:52:54: 1000000 INFO @ Mon, 03 Jun 2019 10:53:01: 2000000 INFO @ Mon, 03 Jun 2019 10:53:02: 2000000 INFO @ Mon, 03 Jun 2019 10:53:04: 2000000 INFO @ Mon, 03 Jun 2019 10:53:09: 3000000 INFO @ Mon, 03 Jun 2019 10:53:11: 3000000 INFO @ Mon, 03 Jun 2019 10:53:13: 3000000 INFO @ Mon, 03 Jun 2019 10:53:18: 4000000 INFO @ Mon, 03 Jun 2019 10:53:19: 4000000 INFO @ Mon, 03 Jun 2019 10:53:23: 4000000 INFO @ Mon, 03 Jun 2019 10:53:27: 5000000 INFO @ Mon, 03 Jun 2019 10:53:29: 5000000 INFO @ Mon, 03 Jun 2019 10:53:33: 5000000 INFO @ Mon, 03 Jun 2019 10:53:35: 6000000 INFO @ Mon, 03 Jun 2019 10:53:37: 6000000 INFO @ Mon, 03 Jun 2019 10:53:42: 6000000 INFO @ Mon, 03 Jun 2019 10:53:44: 7000000 INFO @ Mon, 03 Jun 2019 10:53:46: 7000000 INFO @ Mon, 03 Jun 2019 10:53:52: 8000000 INFO @ Mon, 03 Jun 2019 10:53:52: 7000000 INFO @ Mon, 03 Jun 2019 10:53:55: 8000000 INFO @ Mon, 03 Jun 2019 10:54:00: 9000000 INFO @ Mon, 03 Jun 2019 10:54:02: 8000000 INFO @ Mon, 03 Jun 2019 10:54:04: 9000000 INFO @ Mon, 03 Jun 2019 10:54:08: 10000000 INFO @ Mon, 03 Jun 2019 10:54:12: 9000000 INFO @ Mon, 03 Jun 2019 10:54:13: 10000000 INFO @ Mon, 03 Jun 2019 10:54:17: 11000000 INFO @ Mon, 03 Jun 2019 10:54:21: 11000000 INFO @ Mon, 03 Jun 2019 10:54:22: 10000000 INFO @ Mon, 03 Jun 2019 10:54:25: 12000000 INFO @ Mon, 03 Jun 2019 10:54:29: 12000000 INFO @ Mon, 03 Jun 2019 10:54:32: 11000000 INFO @ Mon, 03 Jun 2019 10:54:33: 13000000 INFO @ Mon, 03 Jun 2019 10:54:37: 13000000 INFO @ Mon, 03 Jun 2019 10:54:41: 14000000 INFO @ Mon, 03 Jun 2019 10:54:41: 12000000 INFO @ Mon, 03 Jun 2019 10:54:46: 14000000 INFO @ Mon, 03 Jun 2019 10:54:49: 15000000 INFO @ Mon, 03 Jun 2019 10:54:51: 13000000 INFO @ Mon, 03 Jun 2019 10:54:56: 15000000 INFO @ Mon, 03 Jun 2019 10:54:58: 16000000 INFO @ Mon, 03 Jun 2019 10:55:01: 14000000 INFO @ Mon, 03 Jun 2019 10:55:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:55:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:55:02: #1 total tags in treatment: 16478855 INFO @ Mon, 03 Jun 2019 10:55:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:55:02: #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 10:55:03: #1 tags after filtering in treatment: 16478855 INFO @ Mon, 03 Jun 2019 10:55:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:55:03: #1 finished! INFO @ Mon, 03 Jun 2019 10:55:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:55:04: #2 number of paired peaks: 412 WARNING @ Mon, 03 Jun 2019 10:55:04: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Mon, 03 Jun 2019 10:55:04: start model_add_line... INFO @ Mon, 03 Jun 2019 10:55:04: start X-correlation... INFO @ Mon, 03 Jun 2019 10:55:04: end of X-cor INFO @ Mon, 03 Jun 2019 10:55:04: #2 finished! INFO @ Mon, 03 Jun 2019 10:55:04: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 10:55:04: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 10:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.20_model.r INFO @ Mon, 03 Jun 2019 10:55:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:55:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:55:05: 16000000 INFO @ Mon, 03 Jun 2019 10:55:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:55:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:55:09: #1 total tags in treatment: 16478855 INFO @ Mon, 03 Jun 2019 10:55:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:55:09: #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 10:55:09: #1 tags after filtering in treatment: 16478855 INFO @ Mon, 03 Jun 2019 10:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:55:09: #1 finished! INFO @ Mon, 03 Jun 2019 10:55:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:55:10: 15000000 INFO @ Mon, 03 Jun 2019 10:55:10: #2 number of paired peaks: 412 WARNING @ Mon, 03 Jun 2019 10:55:10: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Mon, 03 Jun 2019 10:55:10: start model_add_line... INFO @ Mon, 03 Jun 2019 10:55:11: start X-correlation... INFO @ Mon, 03 Jun 2019 10:55:11: end of X-cor INFO @ Mon, 03 Jun 2019 10:55:11: #2 finished! INFO @ Mon, 03 Jun 2019 10:55:11: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 10:55:11: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 10:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.10_model.r INFO @ Mon, 03 Jun 2019 10:55:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:55:19: 16000000 INFO @ Mon, 03 Jun 2019 10:55:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:55:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:55:24: #1 total tags in treatment: 16478855 INFO @ Mon, 03 Jun 2019 10:55:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:55:24: #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 10:55:24: #1 tags after filtering in treatment: 16478855 INFO @ Mon, 03 Jun 2019 10:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:55:24: #1 finished! INFO @ Mon, 03 Jun 2019 10:55:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:55:25: #2 number of paired peaks: 412 WARNING @ Mon, 03 Jun 2019 10:55:25: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Mon, 03 Jun 2019 10:55:25: start model_add_line... INFO @ Mon, 03 Jun 2019 10:55:26: start X-correlation... INFO @ Mon, 03 Jun 2019 10:55:26: end of X-cor INFO @ Mon, 03 Jun 2019 10:55:26: #2 finished! INFO @ Mon, 03 Jun 2019 10:55:26: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 10:55:26: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 10:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.05_model.r INFO @ Mon, 03 Jun 2019 10:55:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:55:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:55:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:56:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:56:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:56:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:56:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.20_summits.bed INFO @ Mon, 03 Jun 2019 10:56:13: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1033 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:56:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:56:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:56:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.10_summits.bed INFO @ Mon, 03 Jun 2019 10:56:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1369 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287927/SRX287927.05_summits.bed INFO @ Mon, 03 Jun 2019 10:56:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1822 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。