Job ID = 6455638 SRX = SRX287947 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:08:22 prefetch.2.10.7: 1) Downloading 'SRR870136'... 2020-06-21T10:08:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:35 prefetch.2.10.7: 'SRR870136' is valid 2020-06-21T10:10:35 prefetch.2.10.7: 1) 'SRR870136' was downloaded successfully Read 11258758 spots for SRR870136/SRR870136.sra Written 11258758 spots for SRR870136/SRR870136.sra 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: 00:03:25 11258758 reads; of these: 11258758 (100.00%) were unpaired; of these: 690865 (6.14%) aligned 0 times 7184227 (63.81%) aligned exactly 1 time 3383666 (30.05%) aligned >1 times 93.86% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1456317 / 10567893 = 0.1378 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.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 @ Sun, 21 Jun 2020 19:17:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:17:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:17:50: 1000000 INFO @ Sun, 21 Jun 2020 19:17:56: 2000000 INFO @ Sun, 21 Jun 2020 19:18:02: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:18:08: 4000000 INFO @ Sun, 21 Jun 2020 19:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.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 @ Sun, 21 Jun 2020 19:18:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:14: 5000000 INFO @ Sun, 21 Jun 2020 19:18:14: 1000000 INFO @ Sun, 21 Jun 2020 19:18:20: 2000000 INFO @ Sun, 21 Jun 2020 19:18:20: 6000000 INFO @ Sun, 21 Jun 2020 19:18:25: 3000000 INFO @ Sun, 21 Jun 2020 19:18:26: 7000000 INFO @ Sun, 21 Jun 2020 19:18:31: 4000000 INFO @ Sun, 21 Jun 2020 19:18:32: 8000000 INFO @ Sun, 21 Jun 2020 19:18:36: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:18:38: 9000000 INFO @ Sun, 21 Jun 2020 19:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.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 @ Sun, 21 Jun 2020 19:18:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:39: #1 total tags in treatment: 9111576 INFO @ Sun, 21 Jun 2020 19:18:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:18:40: #1 tags after filtering in treatment: 9111573 INFO @ Sun, 21 Jun 2020 19:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:18:40: #2 number of paired peaks: 841 WARNING @ Sun, 21 Jun 2020 19:18:40: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Sun, 21 Jun 2020 19:18:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:18:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:18:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:18:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:18:40: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:18:40: #2 alternative fragment length(s) may be 4,42 bps INFO @ Sun, 21 Jun 2020 19:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.05_model.r WARNING @ Sun, 21 Jun 2020 19:18:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:18:40: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Sun, 21 Jun 2020 19:18:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:18:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:18:41: 6000000 INFO @ Sun, 21 Jun 2020 19:18:45: 1000000 INFO @ Sun, 21 Jun 2020 19:18:47: 7000000 INFO @ Sun, 21 Jun 2020 19:18:51: 2000000 INFO @ Sun, 21 Jun 2020 19:18:52: 8000000 INFO @ Sun, 21 Jun 2020 19:18:57: 3000000 INFO @ Sun, 21 Jun 2020 19:18:58: 9000000 INFO @ Sun, 21 Jun 2020 19:18:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:18:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:18:59: #1 total tags in treatment: 9111576 INFO @ Sun, 21 Jun 2020 19:18:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:18:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:18:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:59: #1 tags after filtering in treatment: 9111573 INFO @ Sun, 21 Jun 2020 19:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:18:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:18:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:00: #2 number of paired peaks: 841 WARNING @ Sun, 21 Jun 2020 19:19:00: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:00: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:19:00: #2 alternative fragment length(s) may be 4,42 bps INFO @ Sun, 21 Jun 2020 19:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.10_model.r WARNING @ Sun, 21 Jun 2020 19:19:00: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:00: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Sun, 21 Jun 2020 19:19:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:19:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:04: 4000000 INFO @ Sun, 21 Jun 2020 19:19:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:08: Done! pass1 - making usageList (587 chroms): 2 millis pass2 - checking and writing primary data (2180 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:09: 5000000 INFO @ Sun, 21 Jun 2020 19:19:15: 6000000 INFO @ Sun, 21 Jun 2020 19:19:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:19:21: 7000000 INFO @ Sun, 21 Jun 2020 19:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.10_summits.bed INFO @ Sun, 21 Jun 2020 19:19:27: Done! INFO @ Sun, 21 Jun 2020 19:19:27: 8000000 pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (1788 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:34: 9000000 INFO @ Sun, 21 Jun 2020 19:19:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:34: #1 total tags in treatment: 9111576 INFO @ Sun, 21 Jun 2020 19:19:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:19:35: #1 tags after filtering in treatment: 9111573 INFO @ Sun, 21 Jun 2020 19:19:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:35: #2 number of paired peaks: 841 WARNING @ Sun, 21 Jun 2020 19:19:35: Fewer paired peaks (841) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 841 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:35: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:35: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:35: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:35: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:35: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:19:35: #2 alternative fragment length(s) may be 4,42 bps INFO @ Sun, 21 Jun 2020 19:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.20_model.r WARNING @ Sun, 21 Jun 2020 19:19:35: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:19:35: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Sun, 21 Jun 2020 19:19:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:19:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:19:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287947/SRX287947.20_summits.bed INFO @ Sun, 21 Jun 2020 19:20:02: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 9 millis CompletedMACS2peakCalling