Job ID = 1294841 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:20:37 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' 2019-06-03T01:20:37 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/SRR870127' 2019-06-03T01:20:46 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR870127' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T01:20:46 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T01:23:28 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 ) 2019-06-03T01:29:20 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 ) 2019-06-03T01:29:20 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 : 21,425,213 reads read : 21,425,213 reads written : 21,425,213 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: 00:16:36 21425213 reads; of these: 21425213 (100.00%) were unpaired; of these: 4221668 (19.70%) aligned 0 times 5688826 (26.55%) aligned exactly 1 time 11514719 (53.74%) aligned >1 times 80.30% overall alignment rate Time searching: 00:16:36 Overall time: 00:16:36 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] 9534045 / 17203545 = 0.5542 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 11:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.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 11:04:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:04:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.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 11:04:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:04:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.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 11:04:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:04:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:05:00: 1000000 INFO @ Mon, 03 Jun 2019 11:05:00: 1000000 INFO @ Mon, 03 Jun 2019 11:05:01: 1000000 INFO @ Mon, 03 Jun 2019 11:05:08: 2000000 INFO @ Mon, 03 Jun 2019 11:05:08: 2000000 INFO @ Mon, 03 Jun 2019 11:05:09: 2000000 INFO @ Mon, 03 Jun 2019 11:05:15: 3000000 INFO @ Mon, 03 Jun 2019 11:05:16: 3000000 INFO @ Mon, 03 Jun 2019 11:05:17: 3000000 INFO @ Mon, 03 Jun 2019 11:05:23: 4000000 INFO @ Mon, 03 Jun 2019 11:05:23: 4000000 INFO @ Mon, 03 Jun 2019 11:05:25: 4000000 INFO @ Mon, 03 Jun 2019 11:05:31: 5000000 INFO @ Mon, 03 Jun 2019 11:05:31: 5000000 INFO @ Mon, 03 Jun 2019 11:05:33: 5000000 INFO @ Mon, 03 Jun 2019 11:05:39: 6000000 INFO @ Mon, 03 Jun 2019 11:05:39: 6000000 INFO @ Mon, 03 Jun 2019 11:05:42: 6000000 INFO @ Mon, 03 Jun 2019 11:05:47: 7000000 INFO @ Mon, 03 Jun 2019 11:05:48: 7000000 INFO @ Mon, 03 Jun 2019 11:05:51: 7000000 INFO @ Mon, 03 Jun 2019 11:05:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:52: #1 total tags in treatment: 7669500 INFO @ Mon, 03 Jun 2019 11:05:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:52: #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 11:05:52: #1 tags after filtering in treatment: 7669500 INFO @ Mon, 03 Jun 2019 11:05:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:52: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:53: #2 number of paired peaks: 1394 INFO @ Mon, 03 Jun 2019 11:05:53: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:53: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:53: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:53: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:53: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:05:53: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:05:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.05_model.r WARNING @ Mon, 03 Jun 2019 11:05:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:05:53: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:05:53: #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 11:05:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:05:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:53: #1 total tags in treatment: 7669500 INFO @ Mon, 03 Jun 2019 11:05:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:53: #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 11:05:53: #1 tags after filtering in treatment: 7669500 INFO @ Mon, 03 Jun 2019 11:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:53: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:54: #2 number of paired peaks: 1394 INFO @ Mon, 03 Jun 2019 11:05:54: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:54: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:54: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:54: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:54: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:05:54: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.20_model.r WARNING @ Mon, 03 Jun 2019 11:05:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:05:54: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:05:54: #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 11:05:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:05:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:05:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:05:56: #1 total tags in treatment: 7669500 INFO @ Mon, 03 Jun 2019 11:05:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:05:56: #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 11:05:56: #1 tags after filtering in treatment: 7669500 INFO @ Mon, 03 Jun 2019 11:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:05:56: #1 finished! INFO @ Mon, 03 Jun 2019 11:05:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:05:57: #2 number of paired peaks: 1394 INFO @ Mon, 03 Jun 2019 11:05:57: start model_add_line... INFO @ Mon, 03 Jun 2019 11:05:57: start X-correlation... INFO @ Mon, 03 Jun 2019 11:05:57: end of X-cor INFO @ Mon, 03 Jun 2019 11:05:57: #2 finished! INFO @ Mon, 03 Jun 2019 11:05:57: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 11:05:57: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 11:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.10_model.r WARNING @ Mon, 03 Jun 2019 11:05:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:05:57: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 11:05:57: #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 11:05:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:06:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:06:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.05_summits.bed INFO @ Mon, 03 Jun 2019 11:06:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3318 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.20_summits.bed INFO @ Mon, 03 Jun 2019 11:06:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1801 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287938/SRX287938.10_summits.bed INFO @ Mon, 03 Jun 2019 11:06:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2417 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。