Job ID = 16437339 SRX = SRX12764386 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16665612 spots for SRR16562262/SRR16562262.sra Written 16665612 spots for SRR16562262/SRR16562262.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437436 ("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: 00:02:19 16665612 reads; of these: 16665612 (100.00%) were unpaired; of these: 13994196 (83.97%) aligned 0 times 1911430 (11.47%) aligned exactly 1 time 759986 (4.56%) aligned >1 times 16.03% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 138688 / 2671416 = 0.0519 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.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, 02 Aug 2022 12:25:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:25:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:25:16: 1000000 INFO @ Tue, 02 Aug 2022 12:25:24: 2000000 INFO @ Tue, 02 Aug 2022 12:25:27: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:25:27: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:25:27: #1 total tags in treatment: 2532728 INFO @ Tue, 02 Aug 2022 12:25:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:25:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:25:27: #1 tags after filtering in treatment: 2532728 INFO @ Tue, 02 Aug 2022 12:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:25:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:25:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:25:27: #2 number of paired peaks: 692 WARNING @ Tue, 02 Aug 2022 12:25:27: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 02 Aug 2022 12:25:27: start model_add_line... INFO @ Tue, 02 Aug 2022 12:25:27: start X-correlation... INFO @ Tue, 02 Aug 2022 12:25:27: end of X-cor INFO @ Tue, 02 Aug 2022 12:25:27: #2 finished! INFO @ Tue, 02 Aug 2022 12:25:27: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 12:25:27: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 02 Aug 2022 12:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.05_model.r WARNING @ Tue, 02 Aug 2022 12:25:28: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:25:28: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 02 Aug 2022 12:25:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:25:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:25:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.05_summits.bed INFO @ Tue, 02 Aug 2022 12:25:36: Done! WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (651 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.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, 02 Aug 2022 12:25:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:25:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:25:45: 1000000 INFO @ Tue, 02 Aug 2022 12:25:52: 2000000 INFO @ Tue, 02 Aug 2022 12:25:55: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:25:55: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:25:55: #1 total tags in treatment: 2532728 INFO @ Tue, 02 Aug 2022 12:25:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:25:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:25:55: #1 tags after filtering in treatment: 2532728 INFO @ Tue, 02 Aug 2022 12:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:25:55: #1 finished! INFO @ Tue, 02 Aug 2022 12:25:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:25:55: #2 number of paired peaks: 692 WARNING @ Tue, 02 Aug 2022 12:25:55: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 02 Aug 2022 12:25:55: start model_add_line... INFO @ Tue, 02 Aug 2022 12:25:55: start X-correlation... INFO @ Tue, 02 Aug 2022 12:25:55: end of X-cor INFO @ Tue, 02 Aug 2022 12:25:55: #2 finished! INFO @ Tue, 02 Aug 2022 12:25:55: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 12:25:55: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 02 Aug 2022 12:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.10_model.r WARNING @ Tue, 02 Aug 2022 12:25:56: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:25:56: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 02 Aug 2022 12:25:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:25:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:26:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:26:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:26:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:26:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.10_summits.bed INFO @ Tue, 02 Aug 2022 12:26:04: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 63 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.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, 02 Aug 2022 12:26:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:26:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:26:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:26:22: 2000000 INFO @ Tue, 02 Aug 2022 12:26:25: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:26:25: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:26:25: #1 total tags in treatment: 2532728 INFO @ Tue, 02 Aug 2022 12:26:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:26:25: #1 tags after filtering in treatment: 2532728 INFO @ Tue, 02 Aug 2022 12:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:26:25: #1 finished! INFO @ Tue, 02 Aug 2022 12:26:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:26:25: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:26:25: #2 number of paired peaks: 692 WARNING @ Tue, 02 Aug 2022 12:26:25: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 02 Aug 2022 12:26:25: start model_add_line... INFO @ Tue, 02 Aug 2022 12:26:25: start X-correlation... INFO @ Tue, 02 Aug 2022 12:26:25: end of X-cor INFO @ Tue, 02 Aug 2022 12:26:25: #2 finished! INFO @ Tue, 02 Aug 2022 12:26:25: #2 predicted fragment length is 55 bps INFO @ Tue, 02 Aug 2022 12:26:25: #2 alternative fragment length(s) may be 55 bps INFO @ Tue, 02 Aug 2022 12:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.20_model.r WARNING @ Tue, 02 Aug 2022 12:26:25: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:26:25: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Tue, 02 Aug 2022 12:26:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:26:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:26:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:26:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:26:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:26:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764386/SRX12764386.20_summits.bed INFO @ Tue, 02 Aug 2022 12:26:34: Done! pass1 - making usageList (8 chroms): 5 millis pass2 - checking and writing primary data (119 records, 4 fields): 34 millis CompletedMACS2peakCalling