Job ID = 1294495 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:30:17 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 ) 2019-06-02T23:30:17 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 ) 2019-06-02T23:30:17 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 : 15,241,323 reads read : 15,241,323 reads written : 15,241,323 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: 00:04:18 15241323 reads; of these: 15241323 (100.00%) were unpaired; of these: 524464 (3.44%) aligned 0 times 13183480 (86.50%) aligned exactly 1 time 1533379 (10.06%) aligned >1 times 96.56% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 5237012 / 14716859 = 0.3559 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 08:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.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 08:42:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:42:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.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 08:42:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:42:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.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 08:42:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:42:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:42:59: 1000000 INFO @ Mon, 03 Jun 2019 08:43:00: 1000000 INFO @ Mon, 03 Jun 2019 08:43:01: 1000000 INFO @ Mon, 03 Jun 2019 08:43:06: 2000000 INFO @ Mon, 03 Jun 2019 08:43:08: 2000000 INFO @ Mon, 03 Jun 2019 08:43:09: 2000000 INFO @ Mon, 03 Jun 2019 08:43:13: 3000000 INFO @ Mon, 03 Jun 2019 08:43:16: 3000000 INFO @ Mon, 03 Jun 2019 08:43:17: 3000000 INFO @ Mon, 03 Jun 2019 08:43:20: 4000000 INFO @ Mon, 03 Jun 2019 08:43:24: 4000000 INFO @ Mon, 03 Jun 2019 08:43:25: 4000000 INFO @ Mon, 03 Jun 2019 08:43:27: 5000000 INFO @ Mon, 03 Jun 2019 08:43:31: 5000000 INFO @ Mon, 03 Jun 2019 08:43:34: 5000000 INFO @ Mon, 03 Jun 2019 08:43:34: 6000000 INFO @ Mon, 03 Jun 2019 08:43:39: 6000000 INFO @ Mon, 03 Jun 2019 08:43:41: 7000000 INFO @ Mon, 03 Jun 2019 08:43:42: 6000000 INFO @ Mon, 03 Jun 2019 08:43:47: 7000000 INFO @ Mon, 03 Jun 2019 08:43:48: 8000000 INFO @ Mon, 03 Jun 2019 08:43:50: 7000000 INFO @ Mon, 03 Jun 2019 08:43:55: 8000000 INFO @ Mon, 03 Jun 2019 08:43:55: 9000000 INFO @ Mon, 03 Jun 2019 08:43:58: 8000000 INFO @ Mon, 03 Jun 2019 08:43:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:43:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:43:59: #1 total tags in treatment: 9479847 INFO @ Mon, 03 Jun 2019 08:43:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:43:59: #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 08:43:59: #1 tags after filtering in treatment: 9479847 INFO @ Mon, 03 Jun 2019 08:43:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:43:59: #1 finished! INFO @ Mon, 03 Jun 2019 08:43:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:43:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:44:01: #2 number of paired peaks: 10113 INFO @ Mon, 03 Jun 2019 08:44:01: start model_add_line... INFO @ Mon, 03 Jun 2019 08:44:01: start X-correlation... INFO @ Mon, 03 Jun 2019 08:44:01: end of X-cor INFO @ Mon, 03 Jun 2019 08:44:01: #2 finished! INFO @ Mon, 03 Jun 2019 08:44:01: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 08:44:01: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 08:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.20_model.r INFO @ Mon, 03 Jun 2019 08:44:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:44:02: 9000000 INFO @ Mon, 03 Jun 2019 08:44:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:44:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:44:06: #1 total tags in treatment: 9479847 INFO @ Mon, 03 Jun 2019 08:44:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:44:06: #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 08:44:06: #1 tags after filtering in treatment: 9479847 INFO @ Mon, 03 Jun 2019 08:44:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:44:06: #1 finished! INFO @ Mon, 03 Jun 2019 08:44:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:44:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:44:07: 9000000 INFO @ Mon, 03 Jun 2019 08:44:08: #2 number of paired peaks: 10113 INFO @ Mon, 03 Jun 2019 08:44:08: start model_add_line... INFO @ Mon, 03 Jun 2019 08:44:09: start X-correlation... INFO @ Mon, 03 Jun 2019 08:44:09: end of X-cor INFO @ Mon, 03 Jun 2019 08:44:09: #2 finished! INFO @ Mon, 03 Jun 2019 08:44:09: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 08:44:09: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 08:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.05_model.r INFO @ Mon, 03 Jun 2019 08:44:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:44:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:44:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:44:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:44:11: #1 total tags in treatment: 9479847 INFO @ Mon, 03 Jun 2019 08:44:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:44:11: #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 08:44:11: #1 tags after filtering in treatment: 9479847 INFO @ Mon, 03 Jun 2019 08:44:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:44:11: #1 finished! INFO @ Mon, 03 Jun 2019 08:44:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:44:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:44:13: #2 number of paired peaks: 10113 INFO @ Mon, 03 Jun 2019 08:44:13: start model_add_line... INFO @ Mon, 03 Jun 2019 08:44:13: start X-correlation... INFO @ Mon, 03 Jun 2019 08:44:13: end of X-cor INFO @ Mon, 03 Jun 2019 08:44:13: #2 finished! INFO @ Mon, 03 Jun 2019 08:44:13: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 08:44:13: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 08:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.10_model.r INFO @ Mon, 03 Jun 2019 08:44:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:44:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:44:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:44:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.20_summits.bed INFO @ Mon, 03 Jun 2019 08:44:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6913 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.05_summits.bed INFO @ Mon, 03 Jun 2019 08:44:55: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8613 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287695/SRX287695.10_summits.bed INFO @ Mon, 03 Jun 2019 08:45:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7885 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。