Job ID = 1295180 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T03:20:41 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' 2019-06-03T03:20:41 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/sra13/SRR/000925/SRR947606' 2019-06-03T03:20:50 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR947606' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T03:20:50 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T03:30:41 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 : 18,493,128 reads read : 18,493,128 reads written : 18,493,128 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: 00:07:36 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1125002 (6.08%) aligned 0 times 13121065 (70.95%) aligned exactly 1 time 4247061 (22.97%) aligned >1 times 93.92% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 1481683 / 17368126 = 0.0853 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 12:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.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 12:54:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:54:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.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 12:54:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:54:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.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 12:54:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:54:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:54:34: 1000000 INFO @ Mon, 03 Jun 2019 12:54:34: 1000000 INFO @ Mon, 03 Jun 2019 12:54:34: 1000000 INFO @ Mon, 03 Jun 2019 12:54:44: 2000000 INFO @ Mon, 03 Jun 2019 12:54:44: 2000000 INFO @ Mon, 03 Jun 2019 12:54:44: 2000000 INFO @ Mon, 03 Jun 2019 12:54:53: 3000000 INFO @ Mon, 03 Jun 2019 12:54:53: 3000000 INFO @ Mon, 03 Jun 2019 12:54:53: 3000000 INFO @ Mon, 03 Jun 2019 12:55:02: 4000000 INFO @ Mon, 03 Jun 2019 12:55:02: 4000000 INFO @ Mon, 03 Jun 2019 12:55:04: 4000000 INFO @ Mon, 03 Jun 2019 12:55:12: 5000000 INFO @ Mon, 03 Jun 2019 12:55:12: 5000000 INFO @ Mon, 03 Jun 2019 12:55:14: 5000000 INFO @ Mon, 03 Jun 2019 12:55:22: 6000000 INFO @ Mon, 03 Jun 2019 12:55:22: 6000000 INFO @ Mon, 03 Jun 2019 12:55:24: 6000000 INFO @ Mon, 03 Jun 2019 12:55:32: 7000000 INFO @ Mon, 03 Jun 2019 12:55:32: 7000000 INFO @ Mon, 03 Jun 2019 12:55:36: 7000000 INFO @ Mon, 03 Jun 2019 12:55:43: 8000000 INFO @ Mon, 03 Jun 2019 12:55:43: 8000000 INFO @ Mon, 03 Jun 2019 12:55:46: 8000000 INFO @ Mon, 03 Jun 2019 12:55:52: 9000000 INFO @ Mon, 03 Jun 2019 12:55:52: 9000000 INFO @ Mon, 03 Jun 2019 12:55:55: 9000000 INFO @ Mon, 03 Jun 2019 12:56:02: 10000000 INFO @ Mon, 03 Jun 2019 12:56:02: 10000000 INFO @ Mon, 03 Jun 2019 12:56:05: 10000000 INFO @ Mon, 03 Jun 2019 12:56:10: 11000000 INFO @ Mon, 03 Jun 2019 12:56:10: 11000000 INFO @ Mon, 03 Jun 2019 12:56:16: 11000000 INFO @ Mon, 03 Jun 2019 12:56:20: 12000000 INFO @ Mon, 03 Jun 2019 12:56:20: 12000000 INFO @ Mon, 03 Jun 2019 12:56:25: 12000000 INFO @ Mon, 03 Jun 2019 12:56:29: 13000000 INFO @ Mon, 03 Jun 2019 12:56:29: 13000000 INFO @ Mon, 03 Jun 2019 12:56:35: 13000000 INFO @ Mon, 03 Jun 2019 12:56:39: 14000000 INFO @ Mon, 03 Jun 2019 12:56:39: 14000000 INFO @ Mon, 03 Jun 2019 12:56:46: 14000000 INFO @ Mon, 03 Jun 2019 12:56:50: 15000000 INFO @ Mon, 03 Jun 2019 12:56:50: 15000000 INFO @ Mon, 03 Jun 2019 12:56:56: 15000000 INFO @ Mon, 03 Jun 2019 12:56:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:56:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:56:58: #1 total tags in treatment: 15886443 INFO @ Mon, 03 Jun 2019 12:56:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:56:58: #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 12:56:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:56:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:56:58: #1 total tags in treatment: 15886443 INFO @ Mon, 03 Jun 2019 12:56:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:56:58: #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 12:56:58: #1 tags after filtering in treatment: 15886443 INFO @ Mon, 03 Jun 2019 12:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:56:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:56:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:56:58: #1 tags after filtering in treatment: 15886443 INFO @ Mon, 03 Jun 2019 12:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:56:58: #1 finished! INFO @ Mon, 03 Jun 2019 12:56:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:57:00: #2 number of paired peaks: 160 WARNING @ Mon, 03 Jun 2019 12:57:00: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 03 Jun 2019 12:57:00: start model_add_line... INFO @ Mon, 03 Jun 2019 12:57:00: start X-correlation... INFO @ Mon, 03 Jun 2019 12:57:00: end of X-cor INFO @ Mon, 03 Jun 2019 12:57:00: #2 finished! INFO @ Mon, 03 Jun 2019 12:57:00: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 12:57:00: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 12:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.20_model.r WARNING @ Mon, 03 Jun 2019 12:57:00: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:57:00: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 12:57:00: #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 12:57:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:57:00: #2 number of paired peaks: 160 WARNING @ Mon, 03 Jun 2019 12:57:00: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 03 Jun 2019 12:57:00: start model_add_line... INFO @ Mon, 03 Jun 2019 12:57:00: start X-correlation... INFO @ Mon, 03 Jun 2019 12:57:00: end of X-cor INFO @ Mon, 03 Jun 2019 12:57:00: #2 finished! INFO @ Mon, 03 Jun 2019 12:57:00: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 12:57:00: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 12:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.10_model.r WARNING @ Mon, 03 Jun 2019 12:57:00: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:57:00: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 12:57:00: #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 12:57:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:57:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 12:57:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 12:57:04: #1 total tags in treatment: 15886443 INFO @ Mon, 03 Jun 2019 12:57:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:57:04: #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 12:57:04: #1 tags after filtering in treatment: 15886443 INFO @ Mon, 03 Jun 2019 12:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:57:04: #1 finished! INFO @ Mon, 03 Jun 2019 12:57:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:57:05: #2 number of paired peaks: 160 WARNING @ Mon, 03 Jun 2019 12:57:05: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Mon, 03 Jun 2019 12:57:05: start model_add_line... INFO @ Mon, 03 Jun 2019 12:57:06: start X-correlation... INFO @ Mon, 03 Jun 2019 12:57:06: end of X-cor INFO @ Mon, 03 Jun 2019 12:57:06: #2 finished! INFO @ Mon, 03 Jun 2019 12:57:06: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 12:57:06: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 12:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.05_model.r WARNING @ Mon, 03 Jun 2019 12:57:06: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 12:57:06: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 12:57:06: #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 12:57:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:57:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:57:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:57:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.10_summits.bed INFO @ Mon, 03 Jun 2019 12:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:58:02: Done! INFO @ Mon, 03 Jun 2019 12:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.20_summits.bed INFO @ Mon, 03 Jun 2019 12:58:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1070 records, 4 fields): 4 millis pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1617 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331369/SRX331369.05_summits.bed INFO @ Mon, 03 Jun 2019 12:58:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1987 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。