Job ID = 14166983 SRX = SRX7723716 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20054790 spots for SRR11084672/SRR11084672.sra Written 20054790 spots for SRR11084672/SRR11084672.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167312 ("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: 00:06:53 20054790 reads; of these: 20054790 (100.00%) were unpaired; of these: 12505085 (62.35%) aligned 0 times 5622446 (28.04%) aligned exactly 1 time 1927259 (9.61%) aligned >1 times 37.65% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 2508457 / 7549705 = 0.3323 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 08:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.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 08:33:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:33:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:34:05: 1000000 INFO @ Fri, 10 Dec 2021 08:34:14: 2000000 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 08:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.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 08:34:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:34:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:34:24: 3000000 INFO @ Fri, 10 Dec 2021 08:34:34: 4000000 INFO @ Fri, 10 Dec 2021 08:34:37: 1000000 INFO @ Fri, 10 Dec 2021 08:34:44: 5000000 INFO @ Fri, 10 Dec 2021 08:34:44: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:34:44: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:34:44: #1 total tags in treatment: 5041248 INFO @ Fri, 10 Dec 2021 08:34:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:34:44: #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 08:34:44: #1 tags after filtering in treatment: 5041248 INFO @ Fri, 10 Dec 2021 08:34:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:34:44: #1 finished! INFO @ Fri, 10 Dec 2021 08:34:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:34:44: #2 number of paired peaks: 114 WARNING @ Fri, 10 Dec 2021 08:34:44: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Fri, 10 Dec 2021 08:34:44: start model_add_line... INFO @ Fri, 10 Dec 2021 08:34:45: start X-correlation... INFO @ Fri, 10 Dec 2021 08:34:45: end of X-cor INFO @ Fri, 10 Dec 2021 08:34:45: #2 finished! INFO @ Fri, 10 Dec 2021 08:34:45: #2 predicted fragment length is 120 bps INFO @ Fri, 10 Dec 2021 08:34:45: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 10 Dec 2021 08:34:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_model.r WARNING @ Fri, 10 Dec 2021 08:34:45: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:34:45: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Fri, 10 Dec 2021 08:34:45: #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 08:34:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:34:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:34:50: 2000000 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 08:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.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 08:34:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:34:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:35:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:35:02: 3000000 INFO @ Fri, 10 Dec 2021 08:35:07: 1000000 INFO @ Fri, 10 Dec 2021 08:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_summits.bed INFO @ Fri, 10 Dec 2021 08:35:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (658 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:35:15: 4000000 INFO @ Fri, 10 Dec 2021 08:35:19: 2000000 INFO @ Fri, 10 Dec 2021 08:35:27: 5000000 INFO @ Fri, 10 Dec 2021 08:35:27: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:35:27: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:35:27: #1 total tags in treatment: 5041248 INFO @ Fri, 10 Dec 2021 08:35:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:35:27: #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 08:35:27: #1 tags after filtering in treatment: 5041248 INFO @ Fri, 10 Dec 2021 08:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:35:27: #1 finished! INFO @ Fri, 10 Dec 2021 08:35:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:35:27: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:35:28: #2 number of paired peaks: 114 WARNING @ Fri, 10 Dec 2021 08:35:28: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Fri, 10 Dec 2021 08:35:28: start model_add_line... INFO @ Fri, 10 Dec 2021 08:35:28: start X-correlation... INFO @ Fri, 10 Dec 2021 08:35:28: end of X-cor INFO @ Fri, 10 Dec 2021 08:35:28: #2 finished! INFO @ Fri, 10 Dec 2021 08:35:28: #2 predicted fragment length is 120 bps INFO @ Fri, 10 Dec 2021 08:35:28: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 10 Dec 2021 08:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_model.r WARNING @ Fri, 10 Dec 2021 08:35:28: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:35:28: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Fri, 10 Dec 2021 08:35:28: #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 08:35:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:35:30: 3000000 INFO @ Fri, 10 Dec 2021 08:35:42: 4000000 INFO @ Fri, 10 Dec 2021 08:35:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_summits.bed INFO @ Fri, 10 Dec 2021 08:35:51: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:35:54: 5000000 INFO @ Fri, 10 Dec 2021 08:35:55: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:35:55: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:35:55: #1 total tags in treatment: 5041248 INFO @ Fri, 10 Dec 2021 08:35:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:35:55: #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 08:35:55: #1 tags after filtering in treatment: 5041248 INFO @ Fri, 10 Dec 2021 08:35:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:35:55: #1 finished! INFO @ Fri, 10 Dec 2021 08:35:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:35:55: #2 number of paired peaks: 114 WARNING @ Fri, 10 Dec 2021 08:35:55: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Fri, 10 Dec 2021 08:35:55: start model_add_line... INFO @ Fri, 10 Dec 2021 08:35:55: start X-correlation... INFO @ Fri, 10 Dec 2021 08:35:55: end of X-cor INFO @ Fri, 10 Dec 2021 08:35:55: #2 finished! INFO @ Fri, 10 Dec 2021 08:35:55: #2 predicted fragment length is 120 bps INFO @ Fri, 10 Dec 2021 08:35:55: #2 alternative fragment length(s) may be 120 bps INFO @ Fri, 10 Dec 2021 08:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_model.r WARNING @ Fri, 10 Dec 2021 08:35:55: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:35:55: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Fri, 10 Dec 2021 08:35:55: #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 08:35:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:36:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_summits.bed INFO @ Fri, 10 Dec 2021 08:36:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 3 millis CompletedMACS2peakCalling