Job ID = 1293836 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T17:42:17 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 ) 2019-06-02T17:42:17 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 : 27,923,749 reads read : 27,923,749 reads written : 27,923,749 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: 00:08:29 27923749 reads; of these: 27923749 (100.00%) were unpaired; of these: 2972881 (10.65%) aligned 0 times 17966316 (64.34%) aligned exactly 1 time 6984552 (25.01%) aligned >1 times 89.35% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 11084354 / 24950868 = 0.4442 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 03:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.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 03:05:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.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 03:05:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.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 03:05:43: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:05:43: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:05:51: 1000000 INFO @ Mon, 03 Jun 2019 03:05:51: 1000000 INFO @ Mon, 03 Jun 2019 03:05:53: 1000000 INFO @ Mon, 03 Jun 2019 03:05:58: 2000000 INFO @ Mon, 03 Jun 2019 03:05:59: 2000000 INFO @ Mon, 03 Jun 2019 03:06:02: 2000000 INFO @ Mon, 03 Jun 2019 03:06:06: 3000000 INFO @ Mon, 03 Jun 2019 03:06:06: 3000000 INFO @ Mon, 03 Jun 2019 03:06:12: 3000000 INFO @ Mon, 03 Jun 2019 03:06:14: 4000000 INFO @ Mon, 03 Jun 2019 03:06:14: 4000000 INFO @ Mon, 03 Jun 2019 03:06:21: 4000000 INFO @ Mon, 03 Jun 2019 03:06:21: 5000000 INFO @ Mon, 03 Jun 2019 03:06:21: 5000000 INFO @ Mon, 03 Jun 2019 03:06:29: 6000000 INFO @ Mon, 03 Jun 2019 03:06:29: 6000000 INFO @ Mon, 03 Jun 2019 03:06:30: 5000000 INFO @ Mon, 03 Jun 2019 03:06:36: 7000000 INFO @ Mon, 03 Jun 2019 03:06:37: 7000000 INFO @ Mon, 03 Jun 2019 03:06:39: 6000000 INFO @ Mon, 03 Jun 2019 03:06:44: 8000000 INFO @ Mon, 03 Jun 2019 03:06:44: 8000000 INFO @ Mon, 03 Jun 2019 03:06:49: 7000000 INFO @ Mon, 03 Jun 2019 03:06:52: 9000000 INFO @ Mon, 03 Jun 2019 03:06:52: 9000000 INFO @ Mon, 03 Jun 2019 03:06:59: 8000000 INFO @ Mon, 03 Jun 2019 03:06:59: 10000000 INFO @ Mon, 03 Jun 2019 03:07:00: 10000000 INFO @ Mon, 03 Jun 2019 03:07:07: 11000000 INFO @ Mon, 03 Jun 2019 03:07:07: 11000000 INFO @ Mon, 03 Jun 2019 03:07:08: 9000000 INFO @ Mon, 03 Jun 2019 03:07:14: 12000000 INFO @ Mon, 03 Jun 2019 03:07:15: 12000000 INFO @ Mon, 03 Jun 2019 03:07:18: 10000000 INFO @ Mon, 03 Jun 2019 03:07:21: 13000000 INFO @ Mon, 03 Jun 2019 03:07:22: 13000000 INFO @ Mon, 03 Jun 2019 03:07:27: 11000000 INFO @ Mon, 03 Jun 2019 03:07:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:07:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:07:28: #1 total tags in treatment: 13866514 INFO @ Mon, 03 Jun 2019 03:07:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:28: #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 03:07:28: #1 tags after filtering in treatment: 13866514 INFO @ Mon, 03 Jun 2019 03:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:28: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:28: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:07:28: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:07:28: #1 total tags in treatment: 13866514 INFO @ Mon, 03 Jun 2019 03:07:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:28: #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 03:07:29: #1 tags after filtering in treatment: 13866514 INFO @ Mon, 03 Jun 2019 03:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:29: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:30: #2 number of paired peaks: 2714 INFO @ Mon, 03 Jun 2019 03:07:30: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:30: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:30: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:30: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:30: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 03:07:30: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 03:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.20_model.r INFO @ Mon, 03 Jun 2019 03:07:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:07:30: #2 number of paired peaks: 2714 INFO @ Mon, 03 Jun 2019 03:07:30: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:31: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:31: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:31: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:31: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 03:07:31: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 03:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.05_model.r INFO @ Mon, 03 Jun 2019 03:07:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:07:36: 12000000 INFO @ Mon, 03 Jun 2019 03:07:45: 13000000 INFO @ Mon, 03 Jun 2019 03:07:53: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:07:53: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:07:53: #1 total tags in treatment: 13866514 INFO @ Mon, 03 Jun 2019 03:07:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:07:53: #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 03:07:53: #1 tags after filtering in treatment: 13866514 INFO @ Mon, 03 Jun 2019 03:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:07:53: #1 finished! INFO @ Mon, 03 Jun 2019 03:07:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:07:55: #2 number of paired peaks: 2714 INFO @ Mon, 03 Jun 2019 03:07:55: start model_add_line... INFO @ Mon, 03 Jun 2019 03:07:55: start X-correlation... INFO @ Mon, 03 Jun 2019 03:07:55: end of X-cor INFO @ Mon, 03 Jun 2019 03:07:55: #2 finished! INFO @ Mon, 03 Jun 2019 03:07:55: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 03:07:55: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 03:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.10_model.r INFO @ Mon, 03 Jun 2019 03:07:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:08:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.20_summits.bed INFO @ Mon, 03 Jun 2019 03:08:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7837 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.05_summits.bed INFO @ Mon, 03 Jun 2019 03:08:30: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (14606 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:08:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX128301/SRX128301.10_summits.bed INFO @ Mon, 03 Jun 2019 03:08:56: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10873 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。