Job ID = 1294536 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:44:04 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 ) 2019-06-02T23:46:44 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 ) 2019-06-02T23:46:44 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 : NET - Reading information from the socket failed ) 2019-06-02T23:46:44 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 : NET - Reading information from the socket failed ) 2019-06-02T23:48:03 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 ) 2019-06-02T23:50:50 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 ) spots read : 16,856,264 reads read : 16,856,264 reads written : 16,856,264 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:04 16856264 reads; of these: 16856264 (100.00%) were unpaired; of these: 886541 (5.26%) aligned 0 times 11886776 (70.52%) aligned exactly 1 time 4082947 (24.22%) aligned >1 times 94.74% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 1505777 / 15969723 = 0.0943 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 09:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.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 09:05:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:05:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.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 09:05:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:05:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.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 09:05:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:05:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:05:35: 1000000 INFO @ Mon, 03 Jun 2019 09:05:36: 1000000 INFO @ Mon, 03 Jun 2019 09:05:38: 1000000 INFO @ Mon, 03 Jun 2019 09:05:43: 2000000 INFO @ Mon, 03 Jun 2019 09:05:43: 2000000 INFO @ Mon, 03 Jun 2019 09:05:47: 2000000 INFO @ Mon, 03 Jun 2019 09:05:51: 3000000 INFO @ Mon, 03 Jun 2019 09:05:51: 3000000 INFO @ Mon, 03 Jun 2019 09:05:56: 3000000 INFO @ Mon, 03 Jun 2019 09:05:58: 4000000 INFO @ Mon, 03 Jun 2019 09:05:58: 4000000 INFO @ Mon, 03 Jun 2019 09:06:05: 4000000 INFO @ Mon, 03 Jun 2019 09:06:06: 5000000 INFO @ Mon, 03 Jun 2019 09:06:06: 5000000 INFO @ Mon, 03 Jun 2019 09:06:14: 6000000 INFO @ Mon, 03 Jun 2019 09:06:14: 5000000 INFO @ Mon, 03 Jun 2019 09:06:14: 6000000 INFO @ Mon, 03 Jun 2019 09:06:22: 7000000 INFO @ Mon, 03 Jun 2019 09:06:22: 7000000 INFO @ Mon, 03 Jun 2019 09:06:23: 6000000 INFO @ Mon, 03 Jun 2019 09:06:30: 8000000 INFO @ Mon, 03 Jun 2019 09:06:30: 8000000 INFO @ Mon, 03 Jun 2019 09:06:33: 7000000 INFO @ Mon, 03 Jun 2019 09:06:38: 9000000 INFO @ Mon, 03 Jun 2019 09:06:38: 9000000 INFO @ Mon, 03 Jun 2019 09:06:42: 8000000 INFO @ Mon, 03 Jun 2019 09:06:46: 10000000 INFO @ Mon, 03 Jun 2019 09:06:46: 10000000 INFO @ Mon, 03 Jun 2019 09:06:51: 9000000 INFO @ Mon, 03 Jun 2019 09:06:53: 11000000 INFO @ Mon, 03 Jun 2019 09:06:54: 11000000 INFO @ Mon, 03 Jun 2019 09:07:00: 10000000 INFO @ Mon, 03 Jun 2019 09:07:01: 12000000 INFO @ Mon, 03 Jun 2019 09:07:01: 12000000 INFO @ Mon, 03 Jun 2019 09:07:09: 13000000 INFO @ Mon, 03 Jun 2019 09:07:09: 13000000 INFO @ Mon, 03 Jun 2019 09:07:10: 11000000 INFO @ Mon, 03 Jun 2019 09:07:16: 14000000 INFO @ Mon, 03 Jun 2019 09:07:16: 14000000 INFO @ Mon, 03 Jun 2019 09:07:19: 12000000 INFO @ Mon, 03 Jun 2019 09:07:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:07:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:07:20: #1 total tags in treatment: 14463946 INFO @ Mon, 03 Jun 2019 09:07:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:07:20: #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 09:07:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:07:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:07:20: #1 total tags in treatment: 14463946 INFO @ Mon, 03 Jun 2019 09:07:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:07:20: #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 09:07:20: #1 tags after filtering in treatment: 14463946 INFO @ Mon, 03 Jun 2019 09:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:07:20: #1 finished! INFO @ Mon, 03 Jun 2019 09:07:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:07:20: #1 tags after filtering in treatment: 14463946 INFO @ Mon, 03 Jun 2019 09:07:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:07:20: #1 finished! INFO @ Mon, 03 Jun 2019 09:07:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:07:21: #2 number of paired peaks: 119 WARNING @ Mon, 03 Jun 2019 09:07:21: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 03 Jun 2019 09:07:21: start model_add_line... INFO @ Mon, 03 Jun 2019 09:07:21: start X-correlation... INFO @ Mon, 03 Jun 2019 09:07:21: end of X-cor INFO @ Mon, 03 Jun 2019 09:07:21: #2 finished! INFO @ Mon, 03 Jun 2019 09:07:21: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:07:21: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.10_model.r WARNING @ Mon, 03 Jun 2019 09:07:21: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:07:21: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:07:21: #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 09:07:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:07:22: #2 number of paired peaks: 119 WARNING @ Mon, 03 Jun 2019 09:07:22: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 03 Jun 2019 09:07:22: start model_add_line... INFO @ Mon, 03 Jun 2019 09:07:22: start X-correlation... INFO @ Mon, 03 Jun 2019 09:07:22: end of X-cor INFO @ Mon, 03 Jun 2019 09:07:22: #2 finished! INFO @ Mon, 03 Jun 2019 09:07:22: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:07:22: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.20_model.r WARNING @ Mon, 03 Jun 2019 09:07:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:07:22: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:07:22: #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 09:07:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:07:28: 13000000 INFO @ Mon, 03 Jun 2019 09:07:37: 14000000 INFO @ Mon, 03 Jun 2019 09:07:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:07:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:07:41: #1 total tags in treatment: 14463946 INFO @ Mon, 03 Jun 2019 09:07:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:07:41: #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 09:07:42: #1 tags after filtering in treatment: 14463946 INFO @ Mon, 03 Jun 2019 09:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:07:42: #1 finished! INFO @ Mon, 03 Jun 2019 09:07:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:07:43: #2 number of paired peaks: 119 WARNING @ Mon, 03 Jun 2019 09:07:43: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Mon, 03 Jun 2019 09:07:43: start model_add_line... INFO @ Mon, 03 Jun 2019 09:07:43: start X-correlation... INFO @ Mon, 03 Jun 2019 09:07:43: end of X-cor INFO @ Mon, 03 Jun 2019 09:07:43: #2 finished! INFO @ Mon, 03 Jun 2019 09:07:43: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:07:43: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:07:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.05_model.r WARNING @ Mon, 03 Jun 2019 09:07:43: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:07:43: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:07:43: #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 09:07:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:07:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:08:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:08:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:08:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:08:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:08:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.10_summits.bed INFO @ Mon, 03 Jun 2019 09:08:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1655 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:08:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:08:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:08:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.20_summits.bed INFO @ Mon, 03 Jun 2019 09:08:18: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1161 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:08:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287725/SRX287725.05_summits.bed INFO @ Mon, 03 Jun 2019 09:08:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1951 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。