Job ID = 1308634 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:59:31 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 ) 2019-06-03T13:59:31 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 ) 2019-06-03T13:59:31 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 ) 2019-06-03T14:02:35 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 ) 2019-06-03T14:02:35 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 : 24,330,412 reads read : 48,660,824 reads written : 24,330,412 reads 0-length : 24,330,412 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: 00:07:33 24330412 reads; of these: 24330412 (100.00%) were unpaired; of these: 12937229 (53.17%) aligned 0 times 9003215 (37.00%) aligned exactly 1 time 2389968 (9.82%) aligned >1 times 46.83% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 3466754 / 11393183 = 0.3043 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 23:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.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 23:15:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:15:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.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 23:15:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:15:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.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 23:15:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:15:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:15:18: 1000000 INFO @ Mon, 03 Jun 2019 23:15:18: 1000000 INFO @ Mon, 03 Jun 2019 23:15:19: 1000000 INFO @ Mon, 03 Jun 2019 23:15:27: 2000000 INFO @ Mon, 03 Jun 2019 23:15:27: 2000000 INFO @ Mon, 03 Jun 2019 23:15:29: 2000000 INFO @ Mon, 03 Jun 2019 23:15:35: 3000000 INFO @ Mon, 03 Jun 2019 23:15:35: 3000000 INFO @ Mon, 03 Jun 2019 23:15:38: 3000000 INFO @ Mon, 03 Jun 2019 23:15:44: 4000000 INFO @ Mon, 03 Jun 2019 23:15:44: 4000000 INFO @ Mon, 03 Jun 2019 23:15:48: 4000000 INFO @ Mon, 03 Jun 2019 23:15:52: 5000000 INFO @ Mon, 03 Jun 2019 23:15:52: 5000000 INFO @ Mon, 03 Jun 2019 23:15:57: 5000000 INFO @ Mon, 03 Jun 2019 23:16:01: 6000000 INFO @ Mon, 03 Jun 2019 23:16:01: 6000000 INFO @ Mon, 03 Jun 2019 23:16:06: 6000000 INFO @ Mon, 03 Jun 2019 23:16:09: 7000000 INFO @ Mon, 03 Jun 2019 23:16:09: 7000000 INFO @ Mon, 03 Jun 2019 23:16:16: 7000000 INFO @ Mon, 03 Jun 2019 23:16:17: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:16:17: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:16:17: #1 total tags in treatment: 7926429 INFO @ Mon, 03 Jun 2019 23:16:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:16:17: #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 23:16:17: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:16:17: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:16:17: #1 total tags in treatment: 7926429 INFO @ Mon, 03 Jun 2019 23:16:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:16:17: #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 23:16:17: #1 tags after filtering in treatment: 7926429 INFO @ Mon, 03 Jun 2019 23:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:16:17: #1 finished! INFO @ Mon, 03 Jun 2019 23:16:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:16:17: #1 tags after filtering in treatment: 7926429 INFO @ Mon, 03 Jun 2019 23:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:16:17: #1 finished! INFO @ Mon, 03 Jun 2019 23:16:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:16:18: #2 number of paired peaks: 812 WARNING @ Mon, 03 Jun 2019 23:16:18: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Mon, 03 Jun 2019 23:16:18: start model_add_line... INFO @ Mon, 03 Jun 2019 23:16:18: #2 number of paired peaks: 812 WARNING @ Mon, 03 Jun 2019 23:16:18: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Mon, 03 Jun 2019 23:16:18: start model_add_line... INFO @ Mon, 03 Jun 2019 23:16:18: start X-correlation... INFO @ Mon, 03 Jun 2019 23:16:18: end of X-cor INFO @ Mon, 03 Jun 2019 23:16:18: #2 finished! INFO @ Mon, 03 Jun 2019 23:16:18: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 23:16:18: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 23:16:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.05_model.r WARNING @ Mon, 03 Jun 2019 23:16:18: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:16:18: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 23:16:18: #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 23:16:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:16:18: start X-correlation... INFO @ Mon, 03 Jun 2019 23:16:18: end of X-cor INFO @ Mon, 03 Jun 2019 23:16:18: #2 finished! INFO @ Mon, 03 Jun 2019 23:16:18: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 23:16:18: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 23:16:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.20_model.r WARNING @ Mon, 03 Jun 2019 23:16:18: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:16:18: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 23:16:18: #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 23:16:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:16:25: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:16:25: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:16:25: #1 total tags in treatment: 7926429 INFO @ Mon, 03 Jun 2019 23:16:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:16:25: #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 23:16:25: #1 tags after filtering in treatment: 7926429 INFO @ Mon, 03 Jun 2019 23:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:16:25: #1 finished! INFO @ Mon, 03 Jun 2019 23:16:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:16:26: #2 number of paired peaks: 812 WARNING @ Mon, 03 Jun 2019 23:16:26: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Mon, 03 Jun 2019 23:16:26: start model_add_line... INFO @ Mon, 03 Jun 2019 23:16:26: start X-correlation... INFO @ Mon, 03 Jun 2019 23:16:26: end of X-cor INFO @ Mon, 03 Jun 2019 23:16:26: #2 finished! INFO @ Mon, 03 Jun 2019 23:16:26: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 23:16:26: #2 alternative fragment length(s) may be 68 bps INFO @ Mon, 03 Jun 2019 23:16:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.10_model.r WARNING @ Mon, 03 Jun 2019 23:16:26: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:16:26: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Mon, 03 Jun 2019 23:16:26: #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 23:16:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:16:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:16:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:16:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:16:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:16:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:16:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.20_summits.bed INFO @ Mon, 03 Jun 2019 23:16:52: Done! INFO @ Mon, 03 Jun 2019 23:16:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:16:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.05_peaks.narrowPeak pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (764 records, 4 fields): 4 millis INFO @ Mon, 03 Jun 2019 23:16:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.05_summits.bed CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:16:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2905 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343156/SRX5343156.10_summits.bed INFO @ Mon, 03 Jun 2019 23:17:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1200 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。