Job ID = 16438029 SRX = SRX12261342 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15317338 spots for SRR15972598/SRR15972598.sra Written 15317338 spots for SRR15972598/SRR15972598.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438097 ("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: 00:11:56 15317338 reads; of these: 15317338 (100.00%) were unpaired; of these: 688783 (4.50%) aligned 0 times 9640806 (62.94%) aligned exactly 1 time 4987749 (32.56%) aligned >1 times 95.50% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 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] 7599951 / 14628555 = 0.5195 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 13:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.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 13:35:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:35:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:35:33: 1000000 INFO @ Tue, 02 Aug 2022 13:35:45: 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 13:35:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.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 13:35:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:35:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:35:56: 3000000 INFO @ Tue, 02 Aug 2022 13:36:01: 1000000 INFO @ Tue, 02 Aug 2022 13:36:09: 4000000 INFO @ Tue, 02 Aug 2022 13:36:13: 2000000 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 13:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.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 13:36:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:36:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:36:21: 5000000 INFO @ Tue, 02 Aug 2022 13:36:27: 3000000 INFO @ Tue, 02 Aug 2022 13:36:33: 1000000 INFO @ Tue, 02 Aug 2022 13:36:33: 6000000 INFO @ Tue, 02 Aug 2022 13:36:39: 4000000 INFO @ Tue, 02 Aug 2022 13:36:45: 2000000 INFO @ Tue, 02 Aug 2022 13:36:45: 7000000 INFO @ Tue, 02 Aug 2022 13:36:46: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:36:46: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:36:46: #1 total tags in treatment: 7028604 INFO @ Tue, 02 Aug 2022 13:36:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:36:46: #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 13:36:46: #1 tags after filtering in treatment: 7028604 INFO @ Tue, 02 Aug 2022 13:36:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:36:46: #1 finished! INFO @ Tue, 02 Aug 2022 13:36:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:36:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:36:47: #2 number of paired peaks: 438 WARNING @ Tue, 02 Aug 2022 13:36:47: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 02 Aug 2022 13:36:47: start model_add_line... INFO @ Tue, 02 Aug 2022 13:36:47: start X-correlation... INFO @ Tue, 02 Aug 2022 13:36:47: end of X-cor INFO @ Tue, 02 Aug 2022 13:36:47: #2 finished! INFO @ Tue, 02 Aug 2022 13:36:47: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 13:36:47: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 13:36:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.05_model.r WARNING @ Tue, 02 Aug 2022 13:36:47: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:36:47: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 13:36:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:36:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:36:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:36:51: 5000000 INFO @ Tue, 02 Aug 2022 13:36:57: 3000000 INFO @ Tue, 02 Aug 2022 13:37:03: 6000000 INFO @ Tue, 02 Aug 2022 13:37:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:37:10: 4000000 INFO @ Tue, 02 Aug 2022 13:37:15: 7000000 INFO @ Tue, 02 Aug 2022 13:37:16: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:37:16: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:37:16: #1 total tags in treatment: 7028604 INFO @ Tue, 02 Aug 2022 13:37:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:37:16: #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 13:37:16: #1 tags after filtering in treatment: 7028604 INFO @ Tue, 02 Aug 2022 13:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:37:16: #1 finished! INFO @ Tue, 02 Aug 2022 13:37:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:37:17: #2 number of paired peaks: 438 WARNING @ Tue, 02 Aug 2022 13:37:17: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 02 Aug 2022 13:37:17: start model_add_line... INFO @ Tue, 02 Aug 2022 13:37:17: start X-correlation... INFO @ Tue, 02 Aug 2022 13:37:17: end of X-cor INFO @ Tue, 02 Aug 2022 13:37:17: #2 finished! INFO @ Tue, 02 Aug 2022 13:37:17: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 13:37:17: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 13:37:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.10_model.r WARNING @ Tue, 02 Aug 2022 13:37:17: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:37:17: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 13:37:17: #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 13:37:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:37:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.05_summits.bed INFO @ Tue, 02 Aug 2022 13:37:20: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5482 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:37:22: 5000000 INFO @ Tue, 02 Aug 2022 13:37:34: 6000000 INFO @ Tue, 02 Aug 2022 13:37:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:37:46: 7000000 INFO @ Tue, 02 Aug 2022 13:37:46: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:37:46: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:37:46: #1 total tags in treatment: 7028604 INFO @ Tue, 02 Aug 2022 13:37:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:37:46: #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 13:37:47: #1 tags after filtering in treatment: 7028604 INFO @ Tue, 02 Aug 2022 13:37:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:37:47: #1 finished! INFO @ Tue, 02 Aug 2022 13:37:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:37:47: #2 number of paired peaks: 438 WARNING @ Tue, 02 Aug 2022 13:37:47: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 02 Aug 2022 13:37:47: start model_add_line... INFO @ Tue, 02 Aug 2022 13:37:47: start X-correlation... INFO @ Tue, 02 Aug 2022 13:37:47: end of X-cor INFO @ Tue, 02 Aug 2022 13:37:47: #2 finished! INFO @ Tue, 02 Aug 2022 13:37:47: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 13:37:47: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 13:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.20_model.r WARNING @ Tue, 02 Aug 2022 13:37:47: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:37:47: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 13:37:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:37:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.10_summits.bed INFO @ Tue, 02 Aug 2022 13:37:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1823 records, 4 fields): 306 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:38:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261342/SRX12261342.20_summits.bed INFO @ Tue, 02 Aug 2022 13:38:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (567 records, 4 fields): 25 millis CompletedMACS2peakCalling