Job ID = 1294466 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:11:59 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 ) 2019-06-02T23:11:59 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 ) 2019-06-02T23:13:25 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 ) 2019-06-02T23:13:25 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 ) 2019-06-02T23:13:50 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 ) 2019-06-02T23:15:14 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 ) 2019-06-02T23:16:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 13,007,198 reads read : 13,007,198 reads written : 13,007,198 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: 00:05:50 13007198 reads; of these: 13007198 (100.00%) were unpaired; of these: 657071 (5.05%) aligned 0 times 8587172 (66.02%) aligned exactly 1 time 3762955 (28.93%) aligned >1 times 94.95% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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] 2544152 / 12350127 = 0.2060 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 08:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.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 08:26:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:26:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.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 08:26:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:26:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.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 08:26:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:26:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:26:28: 1000000 INFO @ Mon, 03 Jun 2019 08:26:30: 1000000 INFO @ Mon, 03 Jun 2019 08:26:31: 1000000 INFO @ Mon, 03 Jun 2019 08:26:35: 2000000 INFO @ Mon, 03 Jun 2019 08:26:39: 2000000 INFO @ Mon, 03 Jun 2019 08:26:39: 2000000 INFO @ Mon, 03 Jun 2019 08:26:42: 3000000 INFO @ Mon, 03 Jun 2019 08:26:48: 3000000 INFO @ Mon, 03 Jun 2019 08:26:48: 3000000 INFO @ Mon, 03 Jun 2019 08:26:50: 4000000 INFO @ Mon, 03 Jun 2019 08:26:56: 4000000 INFO @ Mon, 03 Jun 2019 08:26:57: 4000000 INFO @ Mon, 03 Jun 2019 08:26:57: 5000000 INFO @ Mon, 03 Jun 2019 08:27:04: 6000000 INFO @ Mon, 03 Jun 2019 08:27:04: 5000000 INFO @ Mon, 03 Jun 2019 08:27:05: 5000000 INFO @ Mon, 03 Jun 2019 08:27:12: 7000000 INFO @ Mon, 03 Jun 2019 08:27:13: 6000000 INFO @ Mon, 03 Jun 2019 08:27:13: 6000000 INFO @ Mon, 03 Jun 2019 08:27:20: 8000000 INFO @ Mon, 03 Jun 2019 08:27:21: 7000000 INFO @ Mon, 03 Jun 2019 08:27:22: 7000000 INFO @ Mon, 03 Jun 2019 08:27:27: 9000000 INFO @ Mon, 03 Jun 2019 08:27:29: 8000000 INFO @ Mon, 03 Jun 2019 08:27:30: 8000000 INFO @ Mon, 03 Jun 2019 08:27:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:33: #1 total tags in treatment: 9805975 INFO @ Mon, 03 Jun 2019 08:27:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:33: #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 08:27:33: #1 tags after filtering in treatment: 9805975 INFO @ Mon, 03 Jun 2019 08:27:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:33: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:34: #2 number of paired peaks: 436 WARNING @ Mon, 03 Jun 2019 08:27:34: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:34: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:34: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:34: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:34: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:34: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:27:34: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.20_model.r WARNING @ Mon, 03 Jun 2019 08:27:34: #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 08:27:34: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:27:34: #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 08:27:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:27:38: 9000000 INFO @ Mon, 03 Jun 2019 08:27:39: 9000000 INFO @ Mon, 03 Jun 2019 08:27:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:44: #1 total tags in treatment: 9805975 INFO @ Mon, 03 Jun 2019 08:27:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:44: #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 08:27:44: #1 tags after filtering in treatment: 9805975 INFO @ Mon, 03 Jun 2019 08:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:44: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:45: #1 total tags in treatment: 9805975 INFO @ Mon, 03 Jun 2019 08:27:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:45: #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 08:27:45: #2 number of paired peaks: 436 WARNING @ Mon, 03 Jun 2019 08:27:45: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:45: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:45: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:45: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:45: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:45: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:27:45: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.05_model.r WARNING @ Mon, 03 Jun 2019 08:27:45: #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 08:27:45: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:27:45: #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 08:27:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:27:45: #1 tags after filtering in treatment: 9805975 INFO @ Mon, 03 Jun 2019 08:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:45: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:46: #2 number of paired peaks: 436 WARNING @ Mon, 03 Jun 2019 08:27:46: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:46: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:46: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:47: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:47: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:47: #2 predicted fragment length is 46 bps INFO @ Mon, 03 Jun 2019 08:27:47: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 03 Jun 2019 08:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.10_model.r WARNING @ Mon, 03 Jun 2019 08:27:47: #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 08:27:47: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 03 Jun 2019 08:27:47: #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 08:27:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:28:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:28:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:28:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:28:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.20_summits.bed INFO @ Mon, 03 Jun 2019 08:28:16: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1224 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.05_summits.bed INFO @ Mon, 03 Jun 2019 08:28:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2024 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287667/SRX287667.10_summits.bed INFO @ Mon, 03 Jun 2019 08:28:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1695 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。