Job ID = 1295810 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:35:31 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' 2019-06-03T06:35:31 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/sra69/SRR/007525/SRR7706256' 2019-06-03T06:35:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR7706256', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T06:36:14 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' 2019-06-03T06:36:14 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/sra69/SRR/007525/SRR7706256' 2019-06-03T06:36:23 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR7706256' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T06:36:23 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 9,916,105 reads read : 9,916,105 reads written : 9,916,105 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: 00:03:01 9916105 reads; of these: 9916105 (100.00%) were unpaired; of these: 900272 (9.08%) aligned 0 times 7979566 (80.47%) aligned exactly 1 time 1036267 (10.45%) aligned >1 times 90.92% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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_rmdupse_core] 5145836 / 9015833 = 0.5708 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 15:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.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 15:53:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:53:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.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 15:53:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:53:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.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 15:53:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:53:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:53:09: 1000000 INFO @ Mon, 03 Jun 2019 15:53:10: 1000000 INFO @ Mon, 03 Jun 2019 15:53:11: 1000000 INFO @ Mon, 03 Jun 2019 15:53:19: 2000000 INFO @ Mon, 03 Jun 2019 15:53:20: 2000000 INFO @ Mon, 03 Jun 2019 15:53:21: 2000000 INFO @ Mon, 03 Jun 2019 15:53:28: 3000000 INFO @ Mon, 03 Jun 2019 15:53:29: 3000000 INFO @ Mon, 03 Jun 2019 15:53:30: 3000000 INFO @ Mon, 03 Jun 2019 15:53:36: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:53:36: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:53:36: #1 total tags in treatment: 3869997 INFO @ Mon, 03 Jun 2019 15:53:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:53:36: #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 15:53:36: #1 tags after filtering in treatment: 3869997 INFO @ Mon, 03 Jun 2019 15:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:53:36: #1 finished! INFO @ Mon, 03 Jun 2019 15:53:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:53:37: #2 number of paired peaks: 6694 INFO @ Mon, 03 Jun 2019 15:53:37: start model_add_line... INFO @ Mon, 03 Jun 2019 15:53:37: start X-correlation... INFO @ Mon, 03 Jun 2019 15:53:37: end of X-cor INFO @ Mon, 03 Jun 2019 15:53:37: #2 finished! INFO @ Mon, 03 Jun 2019 15:53:37: #2 predicted fragment length is 307 bps INFO @ Mon, 03 Jun 2019 15:53:37: #2 alternative fragment length(s) may be 307 bps INFO @ Mon, 03 Jun 2019 15:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.05_model.r INFO @ Mon, 03 Jun 2019 15:53:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:53:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:53:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:53:37: #1 total tags in treatment: 3869997 INFO @ Mon, 03 Jun 2019 15:53:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:53:37: #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 15:53:37: #1 tags after filtering in treatment: 3869997 INFO @ Mon, 03 Jun 2019 15:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:53:37: #1 finished! INFO @ Mon, 03 Jun 2019 15:53:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:53:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:53:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:53:38: #1 total tags in treatment: 3869997 INFO @ Mon, 03 Jun 2019 15:53:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:53:38: #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 15:53:38: #2 number of paired peaks: 6694 INFO @ Mon, 03 Jun 2019 15:53:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:53:38: #1 tags after filtering in treatment: 3869997 INFO @ Mon, 03 Jun 2019 15:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:53:38: #1 finished! INFO @ Mon, 03 Jun 2019 15:53:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:53:38: start X-correlation... INFO @ Mon, 03 Jun 2019 15:53:38: end of X-cor INFO @ Mon, 03 Jun 2019 15:53:38: #2 finished! INFO @ Mon, 03 Jun 2019 15:53:38: #2 predicted fragment length is 307 bps INFO @ Mon, 03 Jun 2019 15:53:38: #2 alternative fragment length(s) may be 307 bps INFO @ Mon, 03 Jun 2019 15:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.20_model.r INFO @ Mon, 03 Jun 2019 15:53:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:53:39: #2 number of paired peaks: 6694 INFO @ Mon, 03 Jun 2019 15:53:39: start model_add_line... INFO @ Mon, 03 Jun 2019 15:53:39: start X-correlation... INFO @ Mon, 03 Jun 2019 15:53:39: end of X-cor INFO @ Mon, 03 Jun 2019 15:53:39: #2 finished! INFO @ Mon, 03 Jun 2019 15:53:39: #2 predicted fragment length is 307 bps INFO @ Mon, 03 Jun 2019 15:53:39: #2 alternative fragment length(s) may be 307 bps INFO @ Mon, 03 Jun 2019 15:53:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.10_model.r INFO @ Mon, 03 Jun 2019 15:53:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:53:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:53:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:53:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:53:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:54:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.05_summits.bed INFO @ Mon, 03 Jun 2019 15:54:00: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7371 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.20_summits.bed INFO @ Mon, 03 Jun 2019 15:54:01: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4529 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563529/SRX4563529.10_summits.bed INFO @ Mon, 03 Jun 2019 15:54:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5970 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。