Job ID = 10166244 SRX = SRX7723720 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25320946 spots for SRR11084676/SRR11084676.sra Written 25320946 spots for SRR11084676/SRR11084676.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166619 ("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: 00:07:40 25320946 reads; of these: 25320946 (100.00%) were unpaired; of these: 13118019 (51.81%) aligned 0 times 8455778 (33.39%) aligned exactly 1 time 3747149 (14.80%) aligned >1 times 48.19% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4613486 / 12202927 = 0.3781 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.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 @ Thu, 08 Oct 2020 20:54:36: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:54:36: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:54:42: 1000000 INFO @ Thu, 08 Oct 2020 20:54:49: 2000000 INFO @ Thu, 08 Oct 2020 20:54:55: 3000000 INFO @ Thu, 08 Oct 2020 20:55:01: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.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 @ Thu, 08 Oct 2020 20:55:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:55:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:55:08: 5000000 INFO @ Thu, 08 Oct 2020 20:55:11: 1000000 INFO @ Thu, 08 Oct 2020 20:55:16: 6000000 INFO @ Thu, 08 Oct 2020 20:55:19: 2000000 INFO @ Thu, 08 Oct 2020 20:55:23: 7000000 INFO @ Thu, 08 Oct 2020 20:55:26: 3000000 INFO @ Thu, 08 Oct 2020 20:55:27: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:55:27: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:55:27: #1 total tags in treatment: 7589441 INFO @ Thu, 08 Oct 2020 20:55:27: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:55:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:55:27: #1 tags after filtering in treatment: 7589441 INFO @ Thu, 08 Oct 2020 20:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:55:27: #1 finished! INFO @ Thu, 08 Oct 2020 20:55:27: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:55:28: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 20:55:28: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 20:55:28: start model_add_line... INFO @ Thu, 08 Oct 2020 20:55:28: start X-correlation... INFO @ Thu, 08 Oct 2020 20:55:28: end of X-cor INFO @ Thu, 08 Oct 2020 20:55:28: #2 finished! INFO @ Thu, 08 Oct 2020 20:55:28: #2 predicted fragment length is 67 bps INFO @ Thu, 08 Oct 2020 20:55:28: #2 alternative fragment length(s) may be 67 bps INFO @ Thu, 08 Oct 2020 20:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_model.r WARNING @ Thu, 08 Oct 2020 20:55:28: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:55:28: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Thu, 08 Oct 2020 20:55:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:55:28: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:55:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:55:33: 4000000 INFO @ Thu, 08 Oct 2020 20:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.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 @ Thu, 08 Oct 2020 20:55:34: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:55:34: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:55:40: 5000000 INFO @ Thu, 08 Oct 2020 20:55:41: 1000000 INFO @ Thu, 08 Oct 2020 20:55:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:55:48: 6000000 INFO @ Thu, 08 Oct 2020 20:55:49: 2000000 INFO @ Thu, 08 Oct 2020 20:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.05_summits.bed INFO @ Thu, 08 Oct 2020 20:55:52: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1463 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:55:55: 7000000 INFO @ Thu, 08 Oct 2020 20:55:57: 3000000 INFO @ Thu, 08 Oct 2020 20:56:00: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:56:00: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:56:00: #1 total tags in treatment: 7589441 INFO @ Thu, 08 Oct 2020 20:56:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:56:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:56:00: #1 tags after filtering in treatment: 7589441 INFO @ Thu, 08 Oct 2020 20:56:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:56:00: #1 finished! INFO @ Thu, 08 Oct 2020 20:56:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:56:00: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 20:56:00: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 20:56:00: start model_add_line... INFO @ Thu, 08 Oct 2020 20:56:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:56:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:56:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:56:01: #2 predicted fragment length is 67 bps INFO @ Thu, 08 Oct 2020 20:56:01: #2 alternative fragment length(s) may be 67 bps INFO @ Thu, 08 Oct 2020 20:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_model.r WARNING @ Thu, 08 Oct 2020 20:56:01: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:56:01: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Thu, 08 Oct 2020 20:56:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:56:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:56:04: 4000000 INFO @ Thu, 08 Oct 2020 20:56:11: 5000000 INFO @ Thu, 08 Oct 2020 20:56:17: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:56:18: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.10_summits.bed INFO @ Thu, 08 Oct 2020 20:56:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (953 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:56:25: 7000000 INFO @ Thu, 08 Oct 2020 20:56:30: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:56:30: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:56:30: #1 total tags in treatment: 7589441 INFO @ Thu, 08 Oct 2020 20:56:30: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:56:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:56:30: #1 tags after filtering in treatment: 7589441 INFO @ Thu, 08 Oct 2020 20:56:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:56:30: #1 finished! INFO @ Thu, 08 Oct 2020 20:56:30: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:56:30: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 20:56:30: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 20:56:30: start model_add_line... INFO @ Thu, 08 Oct 2020 20:56:30: start X-correlation... INFO @ Thu, 08 Oct 2020 20:56:30: end of X-cor INFO @ Thu, 08 Oct 2020 20:56:30: #2 finished! INFO @ Thu, 08 Oct 2020 20:56:30: #2 predicted fragment length is 67 bps INFO @ Thu, 08 Oct 2020 20:56:30: #2 alternative fragment length(s) may be 67 bps INFO @ Thu, 08 Oct 2020 20:56:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_model.r WARNING @ Thu, 08 Oct 2020 20:56:30: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:56:30: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Thu, 08 Oct 2020 20:56:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:56:30: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:56:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:56:46: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723720/SRX7723720.20_summits.bed INFO @ Thu, 08 Oct 2020 20:56:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 2 millis CompletedMACS2peakCalling