Job ID = 1293628 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:07:55 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 ) 2019-06-02T16:07:55 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 ) 2019-06-02T16:09:33 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 ) spots read : 31,179,457 reads read : 31,179,457 reads written : 31,179,457 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: 00:09:29 31179457 reads; of these: 31179457 (100.00%) were unpaired; of these: 8184285 (26.25%) aligned 0 times 18347118 (58.84%) aligned exactly 1 time 4648054 (14.91%) aligned >1 times 73.75% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 5692203 / 22995172 = 0.2475 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 01:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.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 01:26:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:26:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.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 01:26:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:26:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.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 01:26:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:26:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:26:26: 1000000 INFO @ Mon, 03 Jun 2019 01:26:26: 1000000 INFO @ Mon, 03 Jun 2019 01:26:27: 1000000 INFO @ Mon, 03 Jun 2019 01:26:33: 2000000 INFO @ Mon, 03 Jun 2019 01:26:33: 2000000 INFO @ Mon, 03 Jun 2019 01:26:37: 2000000 INFO @ Mon, 03 Jun 2019 01:26:41: 3000000 INFO @ Mon, 03 Jun 2019 01:26:41: 3000000 INFO @ Mon, 03 Jun 2019 01:26:46: 3000000 INFO @ Mon, 03 Jun 2019 01:26:49: 4000000 INFO @ Mon, 03 Jun 2019 01:26:49: 4000000 INFO @ Mon, 03 Jun 2019 01:26:55: 4000000 INFO @ Mon, 03 Jun 2019 01:26:57: 5000000 INFO @ Mon, 03 Jun 2019 01:26:57: 5000000 INFO @ Mon, 03 Jun 2019 01:27:05: 6000000 INFO @ Mon, 03 Jun 2019 01:27:05: 6000000 INFO @ Mon, 03 Jun 2019 01:27:05: 5000000 INFO @ Mon, 03 Jun 2019 01:27:12: 7000000 INFO @ Mon, 03 Jun 2019 01:27:12: 7000000 INFO @ Mon, 03 Jun 2019 01:27:15: 6000000 INFO @ Mon, 03 Jun 2019 01:27:20: 8000000 INFO @ Mon, 03 Jun 2019 01:27:20: 8000000 INFO @ Mon, 03 Jun 2019 01:27:25: 7000000 INFO @ Mon, 03 Jun 2019 01:27:28: 9000000 INFO @ Mon, 03 Jun 2019 01:27:28: 9000000 INFO @ Mon, 03 Jun 2019 01:27:34: 8000000 INFO @ Mon, 03 Jun 2019 01:27:36: 10000000 INFO @ Mon, 03 Jun 2019 01:27:36: 10000000 INFO @ Mon, 03 Jun 2019 01:27:42: 9000000 INFO @ Mon, 03 Jun 2019 01:27:43: 11000000 INFO @ Mon, 03 Jun 2019 01:27:43: 11000000 INFO @ Mon, 03 Jun 2019 01:27:51: 12000000 INFO @ Mon, 03 Jun 2019 01:27:51: 12000000 INFO @ Mon, 03 Jun 2019 01:27:51: 10000000 INFO @ Mon, 03 Jun 2019 01:27:58: 13000000 INFO @ Mon, 03 Jun 2019 01:27:58: 13000000 INFO @ Mon, 03 Jun 2019 01:28:00: 11000000 INFO @ Mon, 03 Jun 2019 01:28:06: 14000000 INFO @ Mon, 03 Jun 2019 01:28:06: 14000000 INFO @ Mon, 03 Jun 2019 01:28:09: 12000000 INFO @ Mon, 03 Jun 2019 01:28:14: 15000000 INFO @ Mon, 03 Jun 2019 01:28:14: 15000000 INFO @ Mon, 03 Jun 2019 01:28:18: 13000000 INFO @ Mon, 03 Jun 2019 01:28:22: 16000000 INFO @ Mon, 03 Jun 2019 01:28:22: 16000000 INFO @ Mon, 03 Jun 2019 01:28:27: 14000000 INFO @ Mon, 03 Jun 2019 01:28:29: 17000000 INFO @ Mon, 03 Jun 2019 01:28:29: 17000000 INFO @ Mon, 03 Jun 2019 01:28:32: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 01:28:32: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 01:28:32: #1 total tags in treatment: 17302969 INFO @ Mon, 03 Jun 2019 01:28:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:28:32: #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 01:28:32: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 01:28:32: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 01:28:32: #1 total tags in treatment: 17302969 INFO @ Mon, 03 Jun 2019 01:28:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:28:32: #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 01:28:32: #1 tags after filtering in treatment: 17302969 INFO @ Mon, 03 Jun 2019 01:28:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:28:32: #1 finished! INFO @ Mon, 03 Jun 2019 01:28:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:28:32: #1 tags after filtering in treatment: 17302969 INFO @ Mon, 03 Jun 2019 01:28:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:28:32: #1 finished! INFO @ Mon, 03 Jun 2019 01:28:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:28:33: #2 number of paired peaks: 482 WARNING @ Mon, 03 Jun 2019 01:28:33: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Mon, 03 Jun 2019 01:28:33: start model_add_line... INFO @ Mon, 03 Jun 2019 01:28:34: #2 number of paired peaks: 482 WARNING @ Mon, 03 Jun 2019 01:28:34: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Mon, 03 Jun 2019 01:28:34: start model_add_line... INFO @ Mon, 03 Jun 2019 01:28:34: start X-correlation... INFO @ Mon, 03 Jun 2019 01:28:34: end of X-cor INFO @ Mon, 03 Jun 2019 01:28:34: #2 finished! INFO @ Mon, 03 Jun 2019 01:28:34: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 01:28:34: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 01:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.20_model.r INFO @ Mon, 03 Jun 2019 01:28:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:28:34: start X-correlation... INFO @ Mon, 03 Jun 2019 01:28:34: end of X-cor INFO @ Mon, 03 Jun 2019 01:28:34: #2 finished! INFO @ Mon, 03 Jun 2019 01:28:34: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 01:28:34: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 01:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.05_model.r INFO @ Mon, 03 Jun 2019 01:28:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:28:37: 15000000 INFO @ Mon, 03 Jun 2019 01:28:45: 16000000 INFO @ Mon, 03 Jun 2019 01:28:54: 17000000 INFO @ Mon, 03 Jun 2019 01:28:57: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 01:28:57: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 01:28:57: #1 total tags in treatment: 17302969 INFO @ Mon, 03 Jun 2019 01:28:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:28:57: #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 01:28:57: #1 tags after filtering in treatment: 17302969 INFO @ Mon, 03 Jun 2019 01:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:28:57: #1 finished! INFO @ Mon, 03 Jun 2019 01:28:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:28:59: #2 number of paired peaks: 482 WARNING @ Mon, 03 Jun 2019 01:28:59: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Mon, 03 Jun 2019 01:28:59: start model_add_line... INFO @ Mon, 03 Jun 2019 01:28:59: start X-correlation... INFO @ Mon, 03 Jun 2019 01:28:59: end of X-cor INFO @ Mon, 03 Jun 2019 01:28:59: #2 finished! INFO @ Mon, 03 Jun 2019 01:28:59: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 01:28:59: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 01:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.10_model.r INFO @ Mon, 03 Jun 2019 01:28:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:29:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:29:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:29:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:29:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:29:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.20_summits.bed INFO @ Mon, 03 Jun 2019 01:29:44: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (862 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:29:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:29:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:29:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.05_summits.bed INFO @ Mon, 03 Jun 2019 01:29:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3103 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:29:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:30:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:30:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032403/SRX1032403.10_summits.bed INFO @ Mon, 03 Jun 2019 01:30:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1545 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。