Job ID = 6455379 SRX = SRX287740 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:01:40 prefetch.2.10.7: 1) Downloading 'SRR869929'... 2020-06-21T10:01:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:03:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:03:00 prefetch.2.10.7: 'SRR869929' is valid 2020-06-21T10:03:00 prefetch.2.10.7: 1) 'SRR869929' was downloaded successfully Read 9189464 spots for SRR869929/SRR869929.sra Written 9189464 spots for SRR869929/SRR869929.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: 00:03:02 9189464 reads; of these: 9189464 (100.00%) were unpaired; of these: 438469 (4.77%) aligned 0 times 5943394 (64.68%) aligned exactly 1 time 2807601 (30.55%) aligned >1 times 95.23% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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_rmdupse_core] 1751027 / 8750995 = 0.2001 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 19:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.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 19:09:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:16: 1000000 INFO @ Sun, 21 Jun 2020 19:09:21: 2000000 INFO @ Sun, 21 Jun 2020 19:09:27: 3000000 INFO @ Sun, 21 Jun 2020 19:09:33: 4000000 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 19:09:39: 5000000 INFO @ Sun, 21 Jun 2020 19:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.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 19:09:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:46: 6000000 INFO @ Sun, 21 Jun 2020 19:09:46: 1000000 INFO @ Sun, 21 Jun 2020 19:09:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:52: #1 total tags in treatment: 6999968 INFO @ Sun, 21 Jun 2020 19:09:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:52: #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 19:09:53: #1 tags after filtering in treatment: 6999965 INFO @ Sun, 21 Jun 2020 19:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:53: 2000000 INFO @ Sun, 21 Jun 2020 19:09:53: #2 number of paired peaks: 972 WARNING @ Sun, 21 Jun 2020 19:09:53: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Sun, 21 Jun 2020 19:09:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:53: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 19:09:53: #2 alternative fragment length(s) may be 49 bps INFO @ Sun, 21 Jun 2020 19:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.05_model.r WARNING @ Sun, 21 Jun 2020 19:09:53: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:53: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sun, 21 Jun 2020 19:09:53: #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 19:09:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:59: 3000000 INFO @ Sun, 21 Jun 2020 19:10:05: 4000000 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 19:10:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.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 19:10:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:10:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:10:11: 5000000 INFO @ Sun, 21 Jun 2020 19:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.05_summits.bed INFO @ Sun, 21 Jun 2020 19:10:16: Done! INFO @ Sun, 21 Jun 2020 19:10:16: 1000000 pass1 - making usageList (559 chroms): 2 millis pass2 - checking and writing primary data (3092 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:10:18: 6000000 INFO @ Sun, 21 Jun 2020 19:10:23: 2000000 INFO @ Sun, 21 Jun 2020 19:10:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:25: #1 total tags in treatment: 6999968 INFO @ Sun, 21 Jun 2020 19:10:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:25: #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 19:10:25: #1 tags after filtering in treatment: 6999965 INFO @ Sun, 21 Jun 2020 19:10:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:26: #2 number of paired peaks: 972 WARNING @ Sun, 21 Jun 2020 19:10:26: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:26: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 19:10:26: #2 alternative fragment length(s) may be 49 bps INFO @ Sun, 21 Jun 2020 19:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.10_model.r WARNING @ Sun, 21 Jun 2020 19:10:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:26: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sun, 21 Jun 2020 19:10:26: #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 19:10:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:29: 3000000 INFO @ Sun, 21 Jun 2020 19:10:35: 4000000 INFO @ Sun, 21 Jun 2020 19:10:41: 5000000 INFO @ Sun, 21 Jun 2020 19:10:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:10:47: 6000000 INFO @ Sun, 21 Jun 2020 19:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:49: Done! pass1 - making usageList (467 chroms): 1 millis pass2 - checking and writing primary data (1694 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:10:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:53: #1 total tags in treatment: 6999968 INFO @ Sun, 21 Jun 2020 19:10:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:53: #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 19:10:54: #1 tags after filtering in treatment: 6999965 INFO @ Sun, 21 Jun 2020 19:10:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:54: #2 number of paired peaks: 972 WARNING @ Sun, 21 Jun 2020 19:10:54: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Sun, 21 Jun 2020 19:10:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:55: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 19:10:55: #2 alternative fragment length(s) may be 49 bps INFO @ Sun, 21 Jun 2020 19:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.20_model.r WARNING @ Sun, 21 Jun 2020 19:10:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:55: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sun, 21 Jun 2020 19:10:55: #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 19:10:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:11:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287740/SRX287740.20_summits.bed INFO @ Sun, 21 Jun 2020 19:11:18: Done! pass1 - making usageList (291 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 9 millis CompletedMACS2peakCalling