Job ID = 14170490 SRX = SRX8689051 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5680752 spots for SRR12174194/SRR12174194.sra Written 5680752 spots for SRR12174194/SRR12174194.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170889 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:39 5680752 reads; of these: 5680752 (100.00%) were unpaired; of these: 683901 (12.04%) aligned 0 times 3968181 (69.85%) aligned exactly 1 time 1028670 (18.11%) aligned >1 times 87.96% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 167779 / 4996851 = 0.0336 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 06:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.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 06:59:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:59:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:01: 1000000 INFO @ Sat, 11 Dec 2021 07:00:07: 2000000 INFO @ Sat, 11 Dec 2021 07:00:13: 3000000 INFO @ Sat, 11 Dec 2021 07:00:18: 4000000 INFO @ Sat, 11 Dec 2021 07:00:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:23: #1 total tags in treatment: 4829072 INFO @ Sat, 11 Dec 2021 07:00:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:23: #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 07:00:23: #1 tags after filtering in treatment: 4829072 INFO @ Sat, 11 Dec 2021 07:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:23: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:23: #2 number of paired peaks: 345 WARNING @ Sat, 11 Dec 2021 07:00:23: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:23: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:23: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:23: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:23: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:23: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:00:23: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.05_model.r WARNING @ Sat, 11 Dec 2021 07:00:23: #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 07:00:23: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:00:23: #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 07:00:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:23: #3 Pre-compute pvalue-qvalue table... 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 07:00:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.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 07:00:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:31: 1000000 INFO @ Sat, 11 Dec 2021 07:00:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:00:37: 2000000 INFO @ Sat, 11 Dec 2021 07:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.05_summits.bed INFO @ Sat, 11 Dec 2021 07:00:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1247 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:00:42: 3000000 INFO @ Sat, 11 Dec 2021 07:00:48: 4000000 INFO @ Sat, 11 Dec 2021 07:00:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:53: #1 total tags in treatment: 4829072 INFO @ Sat, 11 Dec 2021 07:00:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:53: #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 07:00:53: #1 tags after filtering in treatment: 4829072 INFO @ Sat, 11 Dec 2021 07:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:53: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:53: #2 number of paired peaks: 345 WARNING @ Sat, 11 Dec 2021 07:00:53: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:53: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:53: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:53: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:53: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:53: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:00:53: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:00:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.10_model.r WARNING @ Sat, 11 Dec 2021 07:00:53: #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 07:00:53: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:00:53: #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 07:00:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:53: #3 Pre-compute pvalue-qvalue table... 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 07:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.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 07:00:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:01: 1000000 INFO @ Sat, 11 Dec 2021 07:01:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:06: 2000000 INFO @ Sat, 11 Dec 2021 07:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.10_summits.bed INFO @ Sat, 11 Dec 2021 07:01:08: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:01:10: 3000000 INFO @ Sat, 11 Dec 2021 07:01:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:01:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:19: #1 total tags in treatment: 4829072 INFO @ Sat, 11 Dec 2021 07:01:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:19: #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 07:01:19: #1 tags after filtering in treatment: 4829072 INFO @ Sat, 11 Dec 2021 07:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:19: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:20: #2 number of paired peaks: 345 WARNING @ Sat, 11 Dec 2021 07:01:20: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:20: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:20: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:20: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:20: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:20: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 07:01:20: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 07:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.20_model.r WARNING @ Sat, 11 Dec 2021 07:01:20: #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 07:01:20: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 07:01:20: #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 07:01:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:01:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689051/SRX8689051.20_summits.bed INFO @ Sat, 11 Dec 2021 07:01:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (678 records, 4 fields): 2 millis CompletedMACS2peakCalling