Job ID = 1294621 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:15:29 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' 2019-06-03T00:15:29 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/sra12/SRR/000849/SRR869975' 2019-06-03T00:15:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869975' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:15:38 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T00:17:39 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 ) 2019-06-03T00:17:39 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 ) 2019-06-03T00:17:39 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 ) 2019-06-03T00:27:05 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 ) 2019-06-03T00:27:05 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 ) 2019-06-03T00:27:05 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 ) 2019-06-03T00:33:13 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 : 21,987,706 reads read : 21,987,706 reads written : 21,987,706 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: 00:11:24 21987706 reads; of these: 21987706 (100.00%) were unpaired; of these: 1046727 (4.76%) aligned 0 times 13776997 (62.66%) aligned exactly 1 time 7163982 (32.58%) aligned >1 times 95.24% overall alignment rate Time searching: 00:11:24 Overall time: 00:11:24 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] 2553567 / 20940979 = 0.1219 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 09:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.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 09:59:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:59:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.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 09:59:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:59:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.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 09:59:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:59:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:00:03: 1000000 INFO @ Mon, 03 Jun 2019 10:00:04: 1000000 INFO @ Mon, 03 Jun 2019 10:00:04: 1000000 INFO @ Mon, 03 Jun 2019 10:00:14: 2000000 INFO @ Mon, 03 Jun 2019 10:00:14: 2000000 INFO @ Mon, 03 Jun 2019 10:00:15: 2000000 INFO @ Mon, 03 Jun 2019 10:00:25: 3000000 INFO @ Mon, 03 Jun 2019 10:00:25: 3000000 INFO @ Mon, 03 Jun 2019 10:00:26: 3000000 INFO @ Mon, 03 Jun 2019 10:00:36: 4000000 INFO @ Mon, 03 Jun 2019 10:00:36: 4000000 INFO @ Mon, 03 Jun 2019 10:00:37: 4000000 INFO @ Mon, 03 Jun 2019 10:00:46: 5000000 INFO @ Mon, 03 Jun 2019 10:00:47: 5000000 INFO @ Mon, 03 Jun 2019 10:00:47: 5000000 INFO @ Mon, 03 Jun 2019 10:00:56: 6000000 INFO @ Mon, 03 Jun 2019 10:00:57: 6000000 INFO @ Mon, 03 Jun 2019 10:00:59: 6000000 INFO @ Mon, 03 Jun 2019 10:01:06: 7000000 INFO @ Mon, 03 Jun 2019 10:01:08: 7000000 INFO @ Mon, 03 Jun 2019 10:01:09: 7000000 INFO @ Mon, 03 Jun 2019 10:01:16: 8000000 INFO @ Mon, 03 Jun 2019 10:01:18: 8000000 INFO @ Mon, 03 Jun 2019 10:01:20: 8000000 INFO @ Mon, 03 Jun 2019 10:01:26: 9000000 INFO @ Mon, 03 Jun 2019 10:01:29: 9000000 INFO @ Mon, 03 Jun 2019 10:01:31: 9000000 INFO @ Mon, 03 Jun 2019 10:01:36: 10000000 INFO @ Mon, 03 Jun 2019 10:01:39: 10000000 INFO @ Mon, 03 Jun 2019 10:01:42: 10000000 INFO @ Mon, 03 Jun 2019 10:01:46: 11000000 INFO @ Mon, 03 Jun 2019 10:01:49: 11000000 INFO @ Mon, 03 Jun 2019 10:01:53: 11000000 INFO @ Mon, 03 Jun 2019 10:01:56: 12000000 INFO @ Mon, 03 Jun 2019 10:02:00: 12000000 INFO @ Mon, 03 Jun 2019 10:02:04: 12000000 INFO @ Mon, 03 Jun 2019 10:02:07: 13000000 INFO @ Mon, 03 Jun 2019 10:02:11: 13000000 INFO @ Mon, 03 Jun 2019 10:02:16: 13000000 INFO @ Mon, 03 Jun 2019 10:02:17: 14000000 INFO @ Mon, 03 Jun 2019 10:02:21: 14000000 INFO @ Mon, 03 Jun 2019 10:02:27: 15000000 INFO @ Mon, 03 Jun 2019 10:02:27: 14000000 INFO @ Mon, 03 Jun 2019 10:02:31: 15000000 INFO @ Mon, 03 Jun 2019 10:02:37: 16000000 INFO @ Mon, 03 Jun 2019 10:02:38: 15000000 INFO @ Mon, 03 Jun 2019 10:02:42: 16000000 INFO @ Mon, 03 Jun 2019 10:02:47: 17000000 INFO @ Mon, 03 Jun 2019 10:02:49: 16000000 INFO @ Mon, 03 Jun 2019 10:02:52: 17000000 INFO @ Mon, 03 Jun 2019 10:02:57: 18000000 INFO @ Mon, 03 Jun 2019 10:03:00: 17000000 INFO @ Mon, 03 Jun 2019 10:03:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:03:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:03:01: #1 total tags in treatment: 18387412 INFO @ Mon, 03 Jun 2019 10:03:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:03:01: #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 10:03:01: #1 tags after filtering in treatment: 18387412 INFO @ Mon, 03 Jun 2019 10:03:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:03:01: #1 finished! INFO @ Mon, 03 Jun 2019 10:03:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:03:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:03:02: 18000000 INFO @ Mon, 03 Jun 2019 10:03:03: #2 number of paired peaks: 189 WARNING @ Mon, 03 Jun 2019 10:03:03: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Mon, 03 Jun 2019 10:03:03: start model_add_line... INFO @ Mon, 03 Jun 2019 10:03:03: start X-correlation... INFO @ Mon, 03 Jun 2019 10:03:03: end of X-cor INFO @ Mon, 03 Jun 2019 10:03:03: #2 finished! INFO @ Mon, 03 Jun 2019 10:03:03: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 10:03:03: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 10:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.05_model.r WARNING @ Mon, 03 Jun 2019 10:03:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:03:03: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 10:03:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:03:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:03:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:03:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:03:07: #1 total tags in treatment: 18387412 INFO @ Mon, 03 Jun 2019 10:03:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:03:07: #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 10:03:07: #1 tags after filtering in treatment: 18387412 INFO @ Mon, 03 Jun 2019 10:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:03:07: #1 finished! INFO @ Mon, 03 Jun 2019 10:03:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:03:09: #2 number of paired peaks: 189 WARNING @ Mon, 03 Jun 2019 10:03:09: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Mon, 03 Jun 2019 10:03:09: start model_add_line... INFO @ Mon, 03 Jun 2019 10:03:09: start X-correlation... INFO @ Mon, 03 Jun 2019 10:03:09: end of X-cor INFO @ Mon, 03 Jun 2019 10:03:09: #2 finished! INFO @ Mon, 03 Jun 2019 10:03:09: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 10:03:09: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 10:03:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.10_model.r WARNING @ Mon, 03 Jun 2019 10:03:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:03:09: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 10:03:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:03:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:03:11: 18000000 INFO @ Mon, 03 Jun 2019 10:03:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:03:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:03:15: #1 total tags in treatment: 18387412 INFO @ Mon, 03 Jun 2019 10:03:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:03:15: #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 10:03:15: #1 tags after filtering in treatment: 18387412 INFO @ Mon, 03 Jun 2019 10:03:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:03:15: #1 finished! INFO @ Mon, 03 Jun 2019 10:03:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:03:17: #2 number of paired peaks: 189 WARNING @ Mon, 03 Jun 2019 10:03:17: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Mon, 03 Jun 2019 10:03:17: start model_add_line... INFO @ Mon, 03 Jun 2019 10:03:17: start X-correlation... INFO @ Mon, 03 Jun 2019 10:03:17: end of X-cor INFO @ Mon, 03 Jun 2019 10:03:17: #2 finished! INFO @ Mon, 03 Jun 2019 10:03:17: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 10:03:17: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 10:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.20_model.r WARNING @ Mon, 03 Jun 2019 10:03:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:03:17: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 10:03:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 10:03:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:03:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:03:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:04:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.05_summits.bed INFO @ Mon, 03 Jun 2019 10:04:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2003 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.10_summits.bed INFO @ Mon, 03 Jun 2019 10:04:19: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1564 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287786/SRX287786.20_summits.bed INFO @ Mon, 03 Jun 2019 10:04:28: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1145 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。