Job ID = 14170399 SRX = SRX8689019 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7629140 spots for SRR12174275/SRR12174275.sra Written 7629140 spots for SRR12174275/SRR12174275.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170804 ("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: 00:02:55 7629140 reads; of these: 7629140 (100.00%) were unpaired; of these: 330151 (4.33%) aligned 0 times 4607309 (60.39%) aligned exactly 1 time 2691680 (35.28%) aligned >1 times 95.67% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 514988 / 7298989 = 0.0706 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 06:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.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 06:46:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:46:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:46:50: 1000000 INFO @ Sat, 11 Dec 2021 06:46:56: 2000000 INFO @ Sat, 11 Dec 2021 06:47:01: 3000000 INFO @ Sat, 11 Dec 2021 06:47:07: 4000000 INFO @ Sat, 11 Dec 2021 06:47:12: 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 06:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.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 06:47:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:18: 6000000 INFO @ Sat, 11 Dec 2021 06:47:21: 1000000 INFO @ Sat, 11 Dec 2021 06:47:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:24: #1 total tags in treatment: 6784001 INFO @ Sat, 11 Dec 2021 06:47:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:24: #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 06:47:24: #1 tags after filtering in treatment: 6784001 INFO @ Sat, 11 Dec 2021 06:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:24: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:24: #2 number of paired peaks: 516 WARNING @ Sat, 11 Dec 2021 06:47:24: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:24: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:24: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:24: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:24: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:24: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:47:24: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.05_model.r WARNING @ Sat, 11 Dec 2021 06:47:24: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:24: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:47:24: #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 06:47:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:27: 2000000 INFO @ Sat, 11 Dec 2021 06:47:33: 3000000 INFO @ Sat, 11 Dec 2021 06:47:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:38: 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 @ Sat, 11 Dec 2021 06:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.05_summits.bed INFO @ Sat, 11 Dec 2021 06:47:44: Done! INFO @ Sat, 11 Dec 2021 06:47:44: 5000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1677 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.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 06:47:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:51: 6000000 INFO @ Sat, 11 Dec 2021 06:47:51: 1000000 INFO @ Sat, 11 Dec 2021 06:47:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:56: #1 total tags in treatment: 6784001 INFO @ Sat, 11 Dec 2021 06:47:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:56: #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 06:47:56: #1 tags after filtering in treatment: 6784001 INFO @ Sat, 11 Dec 2021 06:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:56: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:56: #2 number of paired peaks: 516 WARNING @ Sat, 11 Dec 2021 06:47:56: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:56: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:56: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:56: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:56: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:56: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:47:56: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.10_model.r WARNING @ Sat, 11 Dec 2021 06:47:56: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:56: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:47:56: #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 06:47:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:57: 2000000 INFO @ Sat, 11 Dec 2021 06:48:03: 3000000 INFO @ Sat, 11 Dec 2021 06:48:09: 4000000 INFO @ Sat, 11 Dec 2021 06:48:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:14: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:48:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.10_summits.bed INFO @ Sat, 11 Dec 2021 06:48:16: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:20: 6000000 INFO @ Sat, 11 Dec 2021 06:48:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:25: #1 total tags in treatment: 6784001 INFO @ Sat, 11 Dec 2021 06:48:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:25: #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 06:48:25: #1 tags after filtering in treatment: 6784001 INFO @ Sat, 11 Dec 2021 06:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:25: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:25: #2 number of paired peaks: 516 WARNING @ Sat, 11 Dec 2021 06:48:25: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Sat, 11 Dec 2021 06:48:25: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:25: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:25: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:25: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:25: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:48:25: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.20_model.r WARNING @ Sat, 11 Dec 2021 06:48:25: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:48:25: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:48:25: #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 06:48:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:48:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689019/SRX8689019.20_summits.bed INFO @ Sat, 11 Dec 2021 06:48:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (981 records, 4 fields): 11 millis CompletedMACS2peakCalling