Job ID = 16437636 SRX = SRX12261328 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18076691 spots for SRR15972584/SRR15972584.sra Written 18076691 spots for SRR15972584/SRR15972584.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438059 ("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: 00:12:24 18076691 reads; of these: 18076691 (100.00%) were unpaired; of these: 623657 (3.45%) aligned 0 times 11511565 (63.68%) aligned exactly 1 time 5941469 (32.87%) aligned >1 times 96.55% overall alignment rate Time searching: 00:12:24 Overall time: 00:12:24 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_sort_core] merging from 8 files... [bam_rmdupse_core] 11238981 / 17453034 = 0.6440 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 13:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.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 13:23:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:23:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:23:32: 1000000 INFO @ Tue, 02 Aug 2022 13:23:38: 2000000 INFO @ Tue, 02 Aug 2022 13:23:44: 3000000 INFO @ Tue, 02 Aug 2022 13:23:50: 4000000 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 13:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.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 13:23:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:23:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:23:56: 5000000 INFO @ Tue, 02 Aug 2022 13:24:01: 1000000 INFO @ Tue, 02 Aug 2022 13:24:02: 6000000 INFO @ Tue, 02 Aug 2022 13:24:04: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:24:04: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:24:04: #1 total tags in treatment: 6214053 INFO @ Tue, 02 Aug 2022 13:24:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:24:04: #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 13:24:04: #1 tags after filtering in treatment: 6214053 INFO @ Tue, 02 Aug 2022 13:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:24:04: #1 finished! INFO @ Tue, 02 Aug 2022 13:24:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:24:04: #2 number of paired peaks: 957 WARNING @ Tue, 02 Aug 2022 13:24:04: Fewer paired peaks (957) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 957 pairs to build model! INFO @ Tue, 02 Aug 2022 13:24:04: start model_add_line... INFO @ Tue, 02 Aug 2022 13:24:04: start X-correlation... INFO @ Tue, 02 Aug 2022 13:24:04: end of X-cor INFO @ Tue, 02 Aug 2022 13:24:04: #2 finished! INFO @ Tue, 02 Aug 2022 13:24:04: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 13:24:04: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 13:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.05_model.r WARNING @ Tue, 02 Aug 2022 13:24:05: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:24:05: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 13:24:05: #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 13:24:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:24:07: 2000000 INFO @ Tue, 02 Aug 2022 13:24:13: 3000000 INFO @ Tue, 02 Aug 2022 13:24:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:24:20: 4000000 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 13:24:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.05_summits.bed INFO @ Tue, 02 Aug 2022 13:24:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6052 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:24:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.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 13:24:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:24:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:24:26: 5000000 INFO @ Tue, 02 Aug 2022 13:24:32: 1000000 INFO @ Tue, 02 Aug 2022 13:24:33: 6000000 INFO @ Tue, 02 Aug 2022 13:24:35: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:24:35: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:24:35: #1 total tags in treatment: 6214053 INFO @ Tue, 02 Aug 2022 13:24:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:24:35: #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 13:24:35: #1 tags after filtering in treatment: 6214053 INFO @ Tue, 02 Aug 2022 13:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:24:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:24:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:24:35: #2 number of paired peaks: 957 WARNING @ Tue, 02 Aug 2022 13:24:35: Fewer paired peaks (957) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 957 pairs to build model! INFO @ Tue, 02 Aug 2022 13:24:35: start model_add_line... INFO @ Tue, 02 Aug 2022 13:24:36: start X-correlation... INFO @ Tue, 02 Aug 2022 13:24:36: end of X-cor INFO @ Tue, 02 Aug 2022 13:24:36: #2 finished! INFO @ Tue, 02 Aug 2022 13:24:36: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 13:24:36: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 13:24:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.10_model.r WARNING @ Tue, 02 Aug 2022 13:24:36: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:24:36: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 13:24:36: #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 13:24:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:24:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:24:38: 2000000 INFO @ Tue, 02 Aug 2022 13:24:43: 3000000 INFO @ Tue, 02 Aug 2022 13:24:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:24:49: 4000000 INFO @ Tue, 02 Aug 2022 13:24:55: 5000000 INFO @ Tue, 02 Aug 2022 13:24:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:24:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:24:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.10_summits.bed INFO @ Tue, 02 Aug 2022 13:24:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2654 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:25:01: 6000000 INFO @ Tue, 02 Aug 2022 13:25:02: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:25:02: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:25:02: #1 total tags in treatment: 6214053 INFO @ Tue, 02 Aug 2022 13:25:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:25:02: #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 13:25:02: #1 tags after filtering in treatment: 6214053 INFO @ Tue, 02 Aug 2022 13:25:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:25:02: #1 finished! INFO @ Tue, 02 Aug 2022 13:25:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:25:03: #2 number of paired peaks: 957 WARNING @ Tue, 02 Aug 2022 13:25:03: Fewer paired peaks (957) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 957 pairs to build model! INFO @ Tue, 02 Aug 2022 13:25:03: start model_add_line... INFO @ Tue, 02 Aug 2022 13:25:03: start X-correlation... INFO @ Tue, 02 Aug 2022 13:25:03: end of X-cor INFO @ Tue, 02 Aug 2022 13:25:03: #2 finished! INFO @ Tue, 02 Aug 2022 13:25:03: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 13:25:03: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 02 Aug 2022 13:25:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.20_model.r WARNING @ Tue, 02 Aug 2022 13:25:03: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:25:03: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 02 Aug 2022 13:25:03: #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 13:25:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:25:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:25:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261328/SRX12261328.20_summits.bed INFO @ Tue, 02 Aug 2022 13:25:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (709 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。