Job ID = 1294496 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:28:32 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 ) 2019-06-02T23:29:33 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 ) 2019-06-02T23:29:52 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 ) 2019-06-02T23:29:52 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 ) 2019-06-02T23:31:12 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 : 13,900,069 reads read : 13,900,069 reads written : 13,900,069 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: 00:04:36 13900069 reads; of these: 13900069 (100.00%) were unpaired; of these: 562341 (4.05%) aligned 0 times 11463131 (82.47%) aligned exactly 1 time 1874597 (13.49%) aligned >1 times 95.95% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 3866724 / 13337728 = 0.2899 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 08:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.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 08:41:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:41:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.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 08:41:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:41:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.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 08:41:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:41:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:42:03: 1000000 INFO @ Mon, 03 Jun 2019 08:42:05: 1000000 INFO @ Mon, 03 Jun 2019 08:42:05: 1000000 INFO @ Mon, 03 Jun 2019 08:42:11: 2000000 INFO @ Mon, 03 Jun 2019 08:42:15: 2000000 INFO @ Mon, 03 Jun 2019 08:42:15: 2000000 INFO @ Mon, 03 Jun 2019 08:42:19: 3000000 INFO @ Mon, 03 Jun 2019 08:42:24: 3000000 INFO @ Mon, 03 Jun 2019 08:42:24: 3000000 INFO @ Mon, 03 Jun 2019 08:42:26: 4000000 INFO @ Mon, 03 Jun 2019 08:42:33: 5000000 INFO @ Mon, 03 Jun 2019 08:42:33: 4000000 INFO @ Mon, 03 Jun 2019 08:42:33: 4000000 INFO @ Mon, 03 Jun 2019 08:42:40: 6000000 INFO @ Mon, 03 Jun 2019 08:42:42: 5000000 INFO @ Mon, 03 Jun 2019 08:42:42: 5000000 INFO @ Mon, 03 Jun 2019 08:42:46: 7000000 INFO @ Mon, 03 Jun 2019 08:42:51: 6000000 INFO @ Mon, 03 Jun 2019 08:42:51: 6000000 INFO @ Mon, 03 Jun 2019 08:42:53: 8000000 INFO @ Mon, 03 Jun 2019 08:43:00: 7000000 INFO @ Mon, 03 Jun 2019 08:43:00: 7000000 INFO @ Mon, 03 Jun 2019 08:43:00: 9000000 INFO @ Mon, 03 Jun 2019 08:43:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:43:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:43:04: #1 total tags in treatment: 9471004 INFO @ Mon, 03 Jun 2019 08:43:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:43:04: #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 08:43:04: #1 tags after filtering in treatment: 9471004 INFO @ Mon, 03 Jun 2019 08:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:43:04: #1 finished! INFO @ Mon, 03 Jun 2019 08:43:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:43:06: #2 number of paired peaks: 9163 INFO @ Mon, 03 Jun 2019 08:43:06: start model_add_line... INFO @ Mon, 03 Jun 2019 08:43:06: start X-correlation... INFO @ Mon, 03 Jun 2019 08:43:06: end of X-cor INFO @ Mon, 03 Jun 2019 08:43:06: #2 finished! INFO @ Mon, 03 Jun 2019 08:43:06: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 08:43:06: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 08:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.20_model.r INFO @ Mon, 03 Jun 2019 08:43:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:43:09: 8000000 INFO @ Mon, 03 Jun 2019 08:43:09: 8000000 INFO @ Mon, 03 Jun 2019 08:43:18: 9000000 INFO @ Mon, 03 Jun 2019 08:43:18: 9000000 INFO @ Mon, 03 Jun 2019 08:43:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:43:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:43:22: #1 total tags in treatment: 9471004 INFO @ Mon, 03 Jun 2019 08:43:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:43:22: #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 08:43:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:43:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:43:22: #1 total tags in treatment: 9471004 INFO @ Mon, 03 Jun 2019 08:43:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:43:22: #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 08:43:22: #1 tags after filtering in treatment: 9471004 INFO @ Mon, 03 Jun 2019 08:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:43:22: #1 finished! INFO @ Mon, 03 Jun 2019 08:43:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:43:22: #1 tags after filtering in treatment: 9471004 INFO @ Mon, 03 Jun 2019 08:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:43:22: #1 finished! INFO @ Mon, 03 Jun 2019 08:43:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:43:24: #2 number of paired peaks: 9163 INFO @ Mon, 03 Jun 2019 08:43:24: start model_add_line... INFO @ Mon, 03 Jun 2019 08:43:24: #2 number of paired peaks: 9163 INFO @ Mon, 03 Jun 2019 08:43:24: start model_add_line... INFO @ Mon, 03 Jun 2019 08:43:24: start X-correlation... INFO @ Mon, 03 Jun 2019 08:43:24: end of X-cor INFO @ Mon, 03 Jun 2019 08:43:24: #2 finished! INFO @ Mon, 03 Jun 2019 08:43:24: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 08:43:24: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 08:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.10_model.r INFO @ Mon, 03 Jun 2019 08:43:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:43:24: start X-correlation... INFO @ Mon, 03 Jun 2019 08:43:24: end of X-cor INFO @ Mon, 03 Jun 2019 08:43:24: #2 finished! INFO @ Mon, 03 Jun 2019 08:43:24: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 08:43:24: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 08:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.05_model.r INFO @ Mon, 03 Jun 2019 08:43:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:43:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:43:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:43:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:43:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.20_summits.bed INFO @ Mon, 03 Jun 2019 08:43:53: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6255 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:43:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:43:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.10_summits.bed INFO @ Mon, 03 Jun 2019 08:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287696/SRX287696.05_summits.bed INFO @ Mon, 03 Jun 2019 08:44:10: Done! INFO @ Mon, 03 Jun 2019 08:44:10: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7599 records, 4 fields): 12 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8599 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。