Job ID = 14170394 SRX = SRX8689015 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6981984 spots for SRR12174271/SRR12174271.sra Written 6981984 spots for SRR12174271/SRR12174271.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170795 ("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: 00:02:15 6981984 reads; of these: 6981984 (100.00%) were unpaired; of these: 157613 (2.26%) aligned 0 times 4994024 (71.53%) aligned exactly 1 time 1830347 (26.22%) aligned >1 times 97.74% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 239915 / 6824371 = 0.0352 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 @ Sat, 11 Dec 2021 06:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.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 @ Sat, 11 Dec 2021 06:44:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:50: 1000000 INFO @ Sat, 11 Dec 2021 06:44:55: 2000000 INFO @ Sat, 11 Dec 2021 06:45:01: 3000000 INFO @ Sat, 11 Dec 2021 06:45:06: 4000000 INFO @ Sat, 11 Dec 2021 06:45:11: 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 @ Sat, 11 Dec 2021 06:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.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 @ Sat, 11 Dec 2021 06:45:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:17: 6000000 INFO @ Sat, 11 Dec 2021 06:45:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:45:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:45:20: #1 total tags in treatment: 6584456 INFO @ Sat, 11 Dec 2021 06:45:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:45:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:45:20: #1 tags after filtering in treatment: 6584456 INFO @ Sat, 11 Dec 2021 06:45:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:45:20: #1 finished! INFO @ Sat, 11 Dec 2021 06:45:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:45:21: #2 number of paired peaks: 171 WARNING @ Sat, 11 Dec 2021 06:45:21: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 11 Dec 2021 06:45:21: start model_add_line... INFO @ Sat, 11 Dec 2021 06:45:21: start X-correlation... INFO @ Sat, 11 Dec 2021 06:45:21: end of X-cor INFO @ Sat, 11 Dec 2021 06:45:21: #2 finished! INFO @ Sat, 11 Dec 2021 06:45:21: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 06:45:21: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Dec 2021 06:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.05_model.r WARNING @ Sat, 11 Dec 2021 06:45:21: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:45:21: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Dec 2021 06:45:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:45:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:45:22: 1000000 INFO @ Sat, 11 Dec 2021 06:45:28: 2000000 INFO @ Sat, 11 Dec 2021 06:45:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:34: 3000000 INFO @ Sat, 11 Dec 2021 06:45:41: 4000000 INFO @ Sat, 11 Dec 2021 06:45:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.05_summits.bed INFO @ Sat, 11 Dec 2021 06:45:41: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1252 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 06:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.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 @ Sat, 11 Dec 2021 06:45:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:47: 5000000 INFO @ Sat, 11 Dec 2021 06:45:52: 1000000 INFO @ Sat, 11 Dec 2021 06:45:54: 6000000 INFO @ Sat, 11 Dec 2021 06:45:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:45:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:45:58: #1 total tags in treatment: 6584456 INFO @ Sat, 11 Dec 2021 06:45:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:45:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:45:58: #1 tags after filtering in treatment: 6584456 INFO @ Sat, 11 Dec 2021 06:45:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:45:58: #1 finished! INFO @ Sat, 11 Dec 2021 06:45:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:45:58: #2 number of paired peaks: 171 WARNING @ Sat, 11 Dec 2021 06:45:58: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 11 Dec 2021 06:45:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:45:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:45:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:45:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:45:58: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 06:45:58: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Dec 2021 06:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.10_model.r WARNING @ Sat, 11 Dec 2021 06:45:58: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:45:58: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Dec 2021 06:45:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:45:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:45:59: 2000000 INFO @ Sat, 11 Dec 2021 06:46:05: 3000000 INFO @ Sat, 11 Dec 2021 06:46:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:46:12: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.10_summits.bed INFO @ Sat, 11 Dec 2021 06:46:19: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (922 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:46:19: 5000000 INFO @ Sat, 11 Dec 2021 06:46:25: 6000000 INFO @ Sat, 11 Dec 2021 06:46:29: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:46:29: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:46:29: #1 total tags in treatment: 6584456 INFO @ Sat, 11 Dec 2021 06:46:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:46:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:46:29: #1 tags after filtering in treatment: 6584456 INFO @ Sat, 11 Dec 2021 06:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:46:29: #1 finished! INFO @ Sat, 11 Dec 2021 06:46:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:46:29: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:46:30: #2 number of paired peaks: 171 WARNING @ Sat, 11 Dec 2021 06:46:30: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 11 Dec 2021 06:46:30: start model_add_line... INFO @ Sat, 11 Dec 2021 06:46:30: start X-correlation... INFO @ Sat, 11 Dec 2021 06:46:30: end of X-cor INFO @ Sat, 11 Dec 2021 06:46:30: #2 finished! INFO @ Sat, 11 Dec 2021 06:46:30: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 06:46:30: #2 alternative fragment length(s) may be 54 bps INFO @ Sat, 11 Dec 2021 06:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.20_model.r WARNING @ Sat, 11 Dec 2021 06:46:30: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:46:30: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sat, 11 Dec 2021 06:46:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:46:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:46:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:46:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689015/SRX8689015.20_summits.bed INFO @ Sat, 11 Dec 2021 06:46:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 1 millis CompletedMACS2peakCalling