Job ID = 14167253 SRX = SRX8688918 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6635489 spots for SRR12174376/SRR12174376.sra Written 6635489 spots for SRR12174376/SRR12174376.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167852 ("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: 00:02:20 6635489 reads; of these: 6635489 (100.00%) were unpaired; of these: 283920 (4.28%) aligned 0 times 4683902 (70.59%) aligned exactly 1 time 1667667 (25.13%) aligned >1 times 95.72% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 370613 / 6351569 = 0.0583 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 11:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.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 11:24:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:24:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:24:13: 1000000 INFO @ Fri, 10 Dec 2021 11:24:18: 2000000 INFO @ Fri, 10 Dec 2021 11:24:23: 3000000 INFO @ Fri, 10 Dec 2021 11:24:28: 4000000 INFO @ Fri, 10 Dec 2021 11:24:33: 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 11:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.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 11:24:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:24:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:24:38: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:24:38: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:24:38: #1 total tags in treatment: 5980956 INFO @ Fri, 10 Dec 2021 11:24:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:38: #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 11:24:38: #1 tags after filtering in treatment: 5980956 INFO @ Fri, 10 Dec 2021 11:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:24:38: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:38: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:39: #2 number of paired peaks: 218 WARNING @ Fri, 10 Dec 2021 11:24:39: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Fri, 10 Dec 2021 11:24:39: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:39: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:39: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:39: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:39: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:24:39: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.05_model.r WARNING @ Fri, 10 Dec 2021 11:24:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:24:39: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:24:39: #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 11:24:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:43: 1000000 INFO @ Fri, 10 Dec 2021 11:24:49: 2000000 INFO @ Fri, 10 Dec 2021 11:24:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:54: 3000000 INFO @ Fri, 10 Dec 2021 11:24:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.05_summits.bed INFO @ Fri, 10 Dec 2021 11:24:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:24:59: 4000000 INFO @ Fri, 10 Dec 2021 11:25:04: 5000000 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 11:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.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 11:25:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:25:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:25:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:25:10: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:25:10: #1 total tags in treatment: 5980956 INFO @ Fri, 10 Dec 2021 11:25:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:25:10: #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 11:25:10: #1 tags after filtering in treatment: 5980956 INFO @ Fri, 10 Dec 2021 11:25:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:25:10: #1 finished! INFO @ Fri, 10 Dec 2021 11:25:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:25:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:25:10: #2 number of paired peaks: 218 WARNING @ Fri, 10 Dec 2021 11:25:10: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Fri, 10 Dec 2021 11:25:10: start model_add_line... INFO @ Fri, 10 Dec 2021 11:25:10: start X-correlation... INFO @ Fri, 10 Dec 2021 11:25:10: end of X-cor INFO @ Fri, 10 Dec 2021 11:25:10: #2 finished! INFO @ Fri, 10 Dec 2021 11:25:10: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:25:10: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:25:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.10_model.r WARNING @ Fri, 10 Dec 2021 11:25:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:25:10: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:25:10: #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 11:25:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:25:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:25:13: 1000000 INFO @ Fri, 10 Dec 2021 11:25:19: 2000000 INFO @ Fri, 10 Dec 2021 11:25:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:25:24: 3000000 INFO @ Fri, 10 Dec 2021 11:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.10_summits.bed INFO @ Fri, 10 Dec 2021 11:25:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (888 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:25:29: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:25:35: 5000000 INFO @ Fri, 10 Dec 2021 11:25:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:25:40: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:25:40: #1 total tags in treatment: 5980956 INFO @ Fri, 10 Dec 2021 11:25:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:25:40: #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 11:25:40: #1 tags after filtering in treatment: 5980956 INFO @ Fri, 10 Dec 2021 11:25:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:25:40: #1 finished! INFO @ Fri, 10 Dec 2021 11:25:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:25:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:25:41: #2 number of paired peaks: 218 WARNING @ Fri, 10 Dec 2021 11:25:41: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Fri, 10 Dec 2021 11:25:41: start model_add_line... INFO @ Fri, 10 Dec 2021 11:25:41: start X-correlation... INFO @ Fri, 10 Dec 2021 11:25:41: end of X-cor INFO @ Fri, 10 Dec 2021 11:25:41: #2 finished! INFO @ Fri, 10 Dec 2021 11:25:41: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:25:41: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.20_model.r WARNING @ Fri, 10 Dec 2021 11:25:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:25:41: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:25:41: #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 11:25:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:25:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:25:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688918/SRX8688918.20_summits.bed INFO @ Fri, 10 Dec 2021 11:25:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (579 records, 4 fields): 2 millis CompletedMACS2peakCalling