Job ID = 1294457 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:01:17 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 ) 2019-06-02T23:01:17 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 ) 2019-06-02T23:01:17 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 : 9,094,596 reads read : 9,094,596 reads written : 9,094,596 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: 00:05:17 9094596 reads; of these: 9094596 (100.00%) were unpaired; of these: 408816 (4.50%) aligned 0 times 4508876 (49.58%) aligned exactly 1 time 4176904 (45.93%) aligned >1 times 95.50% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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_rmdupse_core] 966381 / 8685780 = 0.1113 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 08:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.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 08:12:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:12:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.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 08:12:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:12:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:12:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.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 08:12:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:12:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:12:26: 1000000 INFO @ Mon, 03 Jun 2019 08:12:27: 1000000 INFO @ Mon, 03 Jun 2019 08:12:27: 1000000 INFO @ Mon, 03 Jun 2019 08:12:33: 2000000 INFO @ Mon, 03 Jun 2019 08:12:36: 2000000 INFO @ Mon, 03 Jun 2019 08:12:36: 2000000 INFO @ Mon, 03 Jun 2019 08:12:42: 3000000 INFO @ Mon, 03 Jun 2019 08:12:46: 3000000 INFO @ Mon, 03 Jun 2019 08:12:46: 3000000 INFO @ Mon, 03 Jun 2019 08:12:51: 4000000 INFO @ Mon, 03 Jun 2019 08:12:54: 4000000 INFO @ Mon, 03 Jun 2019 08:12:55: 4000000 INFO @ Mon, 03 Jun 2019 08:12:59: 5000000 INFO @ Mon, 03 Jun 2019 08:13:04: 5000000 INFO @ Mon, 03 Jun 2019 08:13:05: 5000000 INFO @ Mon, 03 Jun 2019 08:13:07: 6000000 INFO @ Mon, 03 Jun 2019 08:13:14: 6000000 INFO @ Mon, 03 Jun 2019 08:13:15: 6000000 INFO @ Mon, 03 Jun 2019 08:13:16: 7000000 INFO @ Mon, 03 Jun 2019 08:13:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:13:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:13:22: #1 total tags in treatment: 7719399 INFO @ Mon, 03 Jun 2019 08:13:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:13:22: #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 08:13:22: #1 tags after filtering in treatment: 7719399 INFO @ Mon, 03 Jun 2019 08:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:13:22: #1 finished! INFO @ Mon, 03 Jun 2019 08:13:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:13:23: #2 number of paired peaks: 988 WARNING @ Mon, 03 Jun 2019 08:13:23: Fewer paired peaks (988) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 988 pairs to build model! INFO @ Mon, 03 Jun 2019 08:13:23: start model_add_line... INFO @ Mon, 03 Jun 2019 08:13:23: start X-correlation... INFO @ Mon, 03 Jun 2019 08:13:23: end of X-cor INFO @ Mon, 03 Jun 2019 08:13:23: #2 finished! INFO @ Mon, 03 Jun 2019 08:13:23: #2 predicted fragment length is 54 bps INFO @ Mon, 03 Jun 2019 08:13:23: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 03 Jun 2019 08:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.05_model.r WARNING @ Mon, 03 Jun 2019 08:13:23: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:13:23: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 03 Jun 2019 08:13:23: #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 08:13:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:13:24: 7000000 INFO @ Mon, 03 Jun 2019 08:13:25: 7000000 INFO @ Mon, 03 Jun 2019 08:13:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:13:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:13:31: #1 total tags in treatment: 7719399 INFO @ Mon, 03 Jun 2019 08:13:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:13:31: #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 08:13:32: #1 tags after filtering in treatment: 7719399 INFO @ Mon, 03 Jun 2019 08:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:13:32: #1 finished! INFO @ Mon, 03 Jun 2019 08:13:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:13:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:13:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:13:32: #1 total tags in treatment: 7719399 INFO @ Mon, 03 Jun 2019 08:13:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:13:32: #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 08:13:32: #1 tags after filtering in treatment: 7719399 INFO @ Mon, 03 Jun 2019 08:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:13:32: #1 finished! INFO @ Mon, 03 Jun 2019 08:13:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:13:32: #2 number of paired peaks: 988 WARNING @ Mon, 03 Jun 2019 08:13:32: Fewer paired peaks (988) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 988 pairs to build model! INFO @ Mon, 03 Jun 2019 08:13:32: start model_add_line... INFO @ Mon, 03 Jun 2019 08:13:33: start X-correlation... INFO @ Mon, 03 Jun 2019 08:13:33: end of X-cor INFO @ Mon, 03 Jun 2019 08:13:33: #2 finished! INFO @ Mon, 03 Jun 2019 08:13:33: #2 predicted fragment length is 54 bps INFO @ Mon, 03 Jun 2019 08:13:33: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 03 Jun 2019 08:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.20_model.r WARNING @ Mon, 03 Jun 2019 08:13:33: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:13:33: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 03 Jun 2019 08:13:33: #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 08:13:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:13:33: #2 number of paired peaks: 988 WARNING @ Mon, 03 Jun 2019 08:13:33: Fewer paired peaks (988) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 988 pairs to build model! INFO @ Mon, 03 Jun 2019 08:13:33: start model_add_line... INFO @ Mon, 03 Jun 2019 08:13:33: start X-correlation... INFO @ Mon, 03 Jun 2019 08:13:33: end of X-cor INFO @ Mon, 03 Jun 2019 08:13:33: #2 finished! INFO @ Mon, 03 Jun 2019 08:13:33: #2 predicted fragment length is 54 bps INFO @ Mon, 03 Jun 2019 08:13:33: #2 alternative fragment length(s) may be 54 bps INFO @ Mon, 03 Jun 2019 08:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.10_model.r WARNING @ Mon, 03 Jun 2019 08:13:33: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:13:33: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Mon, 03 Jun 2019 08:13:33: #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 08:13:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:13:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:13:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:13:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.05_summits.bed INFO @ Mon, 03 Jun 2019 08:13:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2393 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.20_summits.bed INFO @ Mon, 03 Jun 2019 08:14:06: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287659/SRX287659.10_summits.bed INFO @ Mon, 03 Jun 2019 08:14:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1598 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。