Job ID = 6626540 SRX = SRX6813078 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8040012 spots for SRR10080064/SRR10080064.sra Written 8040012 spots for SRR10080064/SRR10080064.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626660 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:15 8040012 reads; of these: 8040012 (100.00%) were unpaired; of these: 1871320 (23.28%) aligned 0 times 5013918 (62.36%) aligned exactly 1 time 1154774 (14.36%) aligned >1 times 76.72% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 829904 / 6168692 = 0.1345 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 @ Tue, 14 Jul 2020 07:27:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.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 @ Tue, 14 Jul 2020 07:27:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:27:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:27:54: 1000000 INFO @ Tue, 14 Jul 2020 07:28:01: 2000000 INFO @ Tue, 14 Jul 2020 07:28:09: 3000000 INFO @ Tue, 14 Jul 2020 07:28:15: 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 @ Tue, 14 Jul 2020 07:28:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.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 @ Tue, 14 Jul 2020 07:28:18: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:18: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:21: 5000000 INFO @ Tue, 14 Jul 2020 07:28:23: 1000000 INFO @ Tue, 14 Jul 2020 07:28:24: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:28:24: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:28:24: #1 total tags in treatment: 5338788 INFO @ Tue, 14 Jul 2020 07:28:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:28:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:28:24: #1 tags after filtering in treatment: 5338788 INFO @ Tue, 14 Jul 2020 07:28:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:28:24: #1 finished! INFO @ Tue, 14 Jul 2020 07:28:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:28:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:28:24: #2 number of paired peaks: 514 WARNING @ Tue, 14 Jul 2020 07:28:24: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Tue, 14 Jul 2020 07:28:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:28:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:28:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:28:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:28:24: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 07:28:24: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 14 Jul 2020 07:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.05_model.r WARNING @ Tue, 14 Jul 2020 07:28:24: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:28:24: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 14 Jul 2020 07:28:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:28:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:28:29: 2000000 INFO @ Tue, 14 Jul 2020 07:28:34: 3000000 INFO @ Tue, 14 Jul 2020 07:28:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:28:40: 4000000 INFO @ Tue, 14 Jul 2020 07:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.05_summits.bed INFO @ Tue, 14 Jul 2020 07:28:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1534 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:28:45: 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 @ Tue, 14 Jul 2020 07:28:47: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:28:47: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:28:47: #1 total tags in treatment: 5338788 INFO @ Tue, 14 Jul 2020 07:28:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:28:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:28:47: #1 tags after filtering in treatment: 5338788 INFO @ Tue, 14 Jul 2020 07:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:28:47: #1 finished! INFO @ Tue, 14 Jul 2020 07:28:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:28:47: #2 number of paired peaks: 514 WARNING @ Tue, 14 Jul 2020 07:28:47: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Tue, 14 Jul 2020 07:28:47: start model_add_line... INFO @ Tue, 14 Jul 2020 07:28:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:28:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:28:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:28:47: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 07:28:47: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 14 Jul 2020 07:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.10_model.r WARNING @ Tue, 14 Jul 2020 07:28:47: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:28:47: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 14 Jul 2020 07:28:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:28:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.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 @ Tue, 14 Jul 2020 07:28:48: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:48: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:53: 1000000 INFO @ Tue, 14 Jul 2020 07:28:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:28:59: 2000000 INFO @ Tue, 14 Jul 2020 07:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.10_summits.bed INFO @ Tue, 14 Jul 2020 07:29:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:29:14: 4000000 INFO @ Tue, 14 Jul 2020 07:29:19: 5000000 INFO @ Tue, 14 Jul 2020 07:29:20: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:29:20: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:29:20: #1 total tags in treatment: 5338788 INFO @ Tue, 14 Jul 2020 07:29:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:29:20: #1 tags after filtering in treatment: 5338788 INFO @ Tue, 14 Jul 2020 07:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:29:20: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:21: #2 number of paired peaks: 514 WARNING @ Tue, 14 Jul 2020 07:29:21: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Tue, 14 Jul 2020 07:29:21: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:21: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 07:29:21: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 14 Jul 2020 07:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.20_model.r WARNING @ Tue, 14 Jul 2020 07:29:21: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:29:21: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 14 Jul 2020 07:29:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:29:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:29:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813078/SRX6813078.20_summits.bed INFO @ Tue, 14 Jul 2020 07:29:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (234 records, 4 fields): 23 millis CompletedMACS2peakCalling