Job ID = 16437634 SRX = SRX12261326 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21240024 spots for SRR15972582/SRR15972582.sra Written 21240024 spots for SRR15972582/SRR15972582.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438057 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:49 21240024 reads; of these: 21240024 (100.00%) were unpaired; of these: 738876 (3.48%) aligned 0 times 14137763 (66.56%) aligned exactly 1 time 6363385 (29.96%) aligned >1 times 96.52% overall alignment rate Time searching: 00:14:50 Overall time: 00:14:50 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 12 files... [bam_rmdupse_core] 11168122 / 20501148 = 0.5448 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 13:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.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 13:24:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:24:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:24:45: 1000000 INFO @ Tue, 02 Aug 2022 13:24:55: 2000000 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 13:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.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 13:25:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:25:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:25:06: 3000000 INFO @ Tue, 02 Aug 2022 13:25:15: 1000000 INFO @ Tue, 02 Aug 2022 13:25:15: 4000000 INFO @ Tue, 02 Aug 2022 13:25:25: 2000000 INFO @ Tue, 02 Aug 2022 13:25:25: 5000000 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 13:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.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 13:25:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:25:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:25:35: 3000000 INFO @ Tue, 02 Aug 2022 13:25:36: 6000000 INFO @ Tue, 02 Aug 2022 13:25:46: 4000000 INFO @ Tue, 02 Aug 2022 13:25:47: 7000000 INFO @ Tue, 02 Aug 2022 13:25:48: 1000000 INFO @ Tue, 02 Aug 2022 13:25:56: 5000000 INFO @ Tue, 02 Aug 2022 13:25:57: 8000000 INFO @ Tue, 02 Aug 2022 13:26:02: 2000000 INFO @ Tue, 02 Aug 2022 13:26:07: 6000000 INFO @ Tue, 02 Aug 2022 13:26:07: 9000000 INFO @ Tue, 02 Aug 2022 13:26:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:26:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:26:11: #1 total tags in treatment: 9333026 INFO @ Tue, 02 Aug 2022 13:26:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:26:11: #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 13:26:11: #1 tags after filtering in treatment: 9333026 INFO @ Tue, 02 Aug 2022 13:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:26:11: #1 finished! INFO @ Tue, 02 Aug 2022 13:26:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:26:12: #2 number of paired peaks: 254 WARNING @ Tue, 02 Aug 2022 13:26:12: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 02 Aug 2022 13:26:12: start model_add_line... INFO @ Tue, 02 Aug 2022 13:26:12: start X-correlation... INFO @ Tue, 02 Aug 2022 13:26:12: end of X-cor INFO @ Tue, 02 Aug 2022 13:26:12: #2 finished! INFO @ Tue, 02 Aug 2022 13:26:12: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 13:26:12: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 13:26:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.05_model.r WARNING @ Tue, 02 Aug 2022 13:26:12: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:26:12: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 13:26:12: #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 13:26:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:26:16: 3000000 INFO @ Tue, 02 Aug 2022 13:26:17: 7000000 INFO @ Tue, 02 Aug 2022 13:26:28: 8000000 INFO @ Tue, 02 Aug 2022 13:26:29: 4000000 INFO @ Tue, 02 Aug 2022 13:26:39: 9000000 INFO @ Tue, 02 Aug 2022 13:26:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:26:42: 5000000 INFO @ Tue, 02 Aug 2022 13:26:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:26:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:26:42: #1 total tags in treatment: 9333026 INFO @ Tue, 02 Aug 2022 13:26:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:26:42: #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 13:26:42: #1 tags after filtering in treatment: 9333026 INFO @ Tue, 02 Aug 2022 13:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:26:42: #1 finished! INFO @ Tue, 02 Aug 2022 13:26:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:26:43: #2 number of paired peaks: 254 WARNING @ Tue, 02 Aug 2022 13:26:43: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 02 Aug 2022 13:26:43: start model_add_line... INFO @ Tue, 02 Aug 2022 13:26:43: start X-correlation... INFO @ Tue, 02 Aug 2022 13:26:43: end of X-cor INFO @ Tue, 02 Aug 2022 13:26:43: #2 finished! INFO @ Tue, 02 Aug 2022 13:26:43: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 13:26:43: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 13:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.10_model.r WARNING @ Tue, 02 Aug 2022 13:26:43: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:26:43: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 13:26:43: #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 13:26:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:26:54: 6000000 INFO @ Tue, 02 Aug 2022 13:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.05_summits.bed INFO @ Tue, 02 Aug 2022 13:26:54: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (8926 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:27:07: 7000000 INFO @ Tue, 02 Aug 2022 13:27:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:27:19: 8000000 INFO @ Tue, 02 Aug 2022 13:27:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:27:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:27:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.10_summits.bed INFO @ Tue, 02 Aug 2022 13:27:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3778 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:27:32: 9000000 INFO @ Tue, 02 Aug 2022 13:27:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:27:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:27:36: #1 total tags in treatment: 9333026 INFO @ Tue, 02 Aug 2022 13:27:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:27:36: #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 13:27:36: #1 tags after filtering in treatment: 9333026 INFO @ Tue, 02 Aug 2022 13:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:27:36: #1 finished! INFO @ Tue, 02 Aug 2022 13:27:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:27:37: #2 number of paired peaks: 254 WARNING @ Tue, 02 Aug 2022 13:27:37: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 02 Aug 2022 13:27:37: start model_add_line... INFO @ Tue, 02 Aug 2022 13:27:37: start X-correlation... INFO @ Tue, 02 Aug 2022 13:27:37: end of X-cor INFO @ Tue, 02 Aug 2022 13:27:37: #2 finished! INFO @ Tue, 02 Aug 2022 13:27:37: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 13:27:37: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 13:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.20_model.r WARNING @ Tue, 02 Aug 2022 13:27:37: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:27:37: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 13:27:37: #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 13:27:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:28:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261326/SRX12261326.20_summits.bed INFO @ Tue, 02 Aug 2022 13:28:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 39 millis CompletedMACS2peakCalling