Job ID = 14167238 SRX = SRX8688903 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9654001 spots for SRR12174255/SRR12174255.sra Written 9654001 spots for SRR12174255/SRR12174255.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167792 ("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: 00:03:12 9654001 reads; of these: 9654001 (100.00%) were unpaired; of these: 722249 (7.48%) aligned 0 times 6450137 (66.81%) aligned exactly 1 time 2481615 (25.71%) aligned >1 times 92.52% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 427947 / 8931752 = 0.0479 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.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 @ Fri, 10 Dec 2021 11:17:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:17:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:18:03: 1000000 INFO @ Fri, 10 Dec 2021 11:18:08: 2000000 INFO @ Fri, 10 Dec 2021 11:18:14: 3000000 INFO @ Fri, 10 Dec 2021 11:18:19: 4000000 INFO @ Fri, 10 Dec 2021 11:18:25: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.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 @ Fri, 10 Dec 2021 11:18:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:18:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:18:30: 6000000 INFO @ Fri, 10 Dec 2021 11:18:34: 1000000 INFO @ Fri, 10 Dec 2021 11:18:37: 7000000 INFO @ Fri, 10 Dec 2021 11:18:40: 2000000 INFO @ Fri, 10 Dec 2021 11:18:43: 8000000 INFO @ Fri, 10 Dec 2021 11:18:46: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:18:46: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:18:46: #1 total tags in treatment: 8503805 INFO @ Fri, 10 Dec 2021 11:18:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:18:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:18:46: #1 tags after filtering in treatment: 8503805 INFO @ Fri, 10 Dec 2021 11:18:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:18:46: #1 finished! INFO @ Fri, 10 Dec 2021 11:18:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:18:46: 3000000 INFO @ Fri, 10 Dec 2021 11:18:47: #2 number of paired peaks: 152 WARNING @ Fri, 10 Dec 2021 11:18:47: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Fri, 10 Dec 2021 11:18:47: start model_add_line... INFO @ Fri, 10 Dec 2021 11:18:47: start X-correlation... INFO @ Fri, 10 Dec 2021 11:18:47: end of X-cor INFO @ Fri, 10 Dec 2021 11:18:47: #2 finished! INFO @ Fri, 10 Dec 2021 11:18:47: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 11:18:47: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 11:18:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.05_model.r WARNING @ Fri, 10 Dec 2021 11:18:47: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:18:47: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 11:18:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:18:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:18:52: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.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 @ Fri, 10 Dec 2021 11:18:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:18:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:18:58: 5000000 INFO @ Fri, 10 Dec 2021 11:19:03: 1000000 INFO @ Fri, 10 Dec 2021 11:19:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:19:04: 6000000 INFO @ Fri, 10 Dec 2021 11:19:10: 2000000 INFO @ Fri, 10 Dec 2021 11:19:11: 7000000 INFO @ Fri, 10 Dec 2021 11:19:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:19:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:19:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.05_summits.bed INFO @ Fri, 10 Dec 2021 11:19:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1304 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:19:16: 3000000 INFO @ Fri, 10 Dec 2021 11:19:17: 8000000 INFO @ Fri, 10 Dec 2021 11:19:20: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:19:20: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:19:20: #1 total tags in treatment: 8503805 INFO @ Fri, 10 Dec 2021 11:19:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:19:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:19:20: #1 tags after filtering in treatment: 8503805 INFO @ Fri, 10 Dec 2021 11:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:19:20: #1 finished! INFO @ Fri, 10 Dec 2021 11:19:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:19:21: #2 number of paired peaks: 152 WARNING @ Fri, 10 Dec 2021 11:19:21: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Fri, 10 Dec 2021 11:19:21: start model_add_line... INFO @ Fri, 10 Dec 2021 11:19:21: start X-correlation... INFO @ Fri, 10 Dec 2021 11:19:21: end of X-cor INFO @ Fri, 10 Dec 2021 11:19:21: #2 finished! INFO @ Fri, 10 Dec 2021 11:19:21: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 11:19:21: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 11:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.10_model.r WARNING @ Fri, 10 Dec 2021 11:19:21: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:19:21: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 11:19:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:19:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:19:22: 4000000 INFO @ Fri, 10 Dec 2021 11:19:28: 5000000 INFO @ Fri, 10 Dec 2021 11:19:34: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:19:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:19:39: 7000000 INFO @ Fri, 10 Dec 2021 11:19:45: 8000000 INFO @ Fri, 10 Dec 2021 11:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.10_summits.bed INFO @ Fri, 10 Dec 2021 11:19:46: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1015 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:19:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:19:48: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:19:48: #1 total tags in treatment: 8503805 INFO @ Fri, 10 Dec 2021 11:19:48: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:19:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:19:48: #1 tags after filtering in treatment: 8503805 INFO @ Fri, 10 Dec 2021 11:19:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:19:48: #1 finished! INFO @ Fri, 10 Dec 2021 11:19:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:19:48: #2 number of paired peaks: 152 WARNING @ Fri, 10 Dec 2021 11:19:48: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Fri, 10 Dec 2021 11:19:48: start model_add_line... INFO @ Fri, 10 Dec 2021 11:19:48: start X-correlation... INFO @ Fri, 10 Dec 2021 11:19:48: end of X-cor INFO @ Fri, 10 Dec 2021 11:19:48: #2 finished! INFO @ Fri, 10 Dec 2021 11:19:48: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 11:19:48: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 11:19:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.20_model.r WARNING @ Fri, 10 Dec 2021 11:19:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:19:48: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 11:19:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:19:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:19:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:20:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688903/SRX8688903.20_summits.bed INFO @ Fri, 10 Dec 2021 11:20:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (722 records, 4 fields): 18 millis CompletedMACS2peakCalling