Job ID = 10165831 SRX = SRX7723685 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29202893 spots for SRR11084641/SRR11084641.sra Written 29202893 spots for SRR11084641/SRR11084641.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166241 ("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: 00:15:03 29202893 reads; of these: 29202893 (100.00%) were unpaired; of these: 4223472 (14.46%) aligned 0 times 17892307 (61.27%) aligned exactly 1 time 7087114 (24.27%) aligned >1 times 85.54% overall alignment rate Time searching: 00:15:03 Overall time: 00:15:03 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 12 files... [bam_rmdupse_core] 12557699 / 24979421 = 0.5027 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 20:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.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 20:19:33: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:19:33: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:19:39: 1000000 INFO @ Thu, 08 Oct 2020 20:19:44: 2000000 INFO @ Thu, 08 Oct 2020 20:19:50: 3000000 INFO @ Thu, 08 Oct 2020 20:19:55: 4000000 INFO @ Thu, 08 Oct 2020 20:20:00: 5000000 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 20:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.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 20:20:03: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:03: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:20:06: 6000000 INFO @ Thu, 08 Oct 2020 20:20:10: 1000000 INFO @ Thu, 08 Oct 2020 20:20:11: 7000000 INFO @ Thu, 08 Oct 2020 20:20:17: 8000000 INFO @ Thu, 08 Oct 2020 20:20:18: 2000000 INFO @ Thu, 08 Oct 2020 20:20:23: 9000000 INFO @ Thu, 08 Oct 2020 20:20:25: 3000000 INFO @ Thu, 08 Oct 2020 20:20:29: 10000000 BedGraph に変換中... INFO @ Thu, 08 Oct 2020 20:20:32: 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 20:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.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 20:20:33: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:33: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:20:35: 11000000 INFO @ Thu, 08 Oct 2020 20:20:38: 5000000 INFO @ Thu, 08 Oct 2020 20:20:40: 1000000 INFO @ Thu, 08 Oct 2020 20:20:42: 12000000 INFO @ Thu, 08 Oct 2020 20:20:44: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:20:44: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:20:44: #1 total tags in treatment: 12421722 INFO @ Thu, 08 Oct 2020 20:20:44: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:20:44: #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 20:20:44: #1 tags after filtering in treatment: 12421722 INFO @ Thu, 08 Oct 2020 20:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:20:44: #1 finished! INFO @ Thu, 08 Oct 2020 20:20:44: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:20:45: 6000000 INFO @ Thu, 08 Oct 2020 20:20:45: #2 number of paired peaks: 261 WARNING @ Thu, 08 Oct 2020 20:20:45: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Thu, 08 Oct 2020 20:20:45: start model_add_line... INFO @ Thu, 08 Oct 2020 20:20:45: start X-correlation... INFO @ Thu, 08 Oct 2020 20:20:45: end of X-cor INFO @ Thu, 08 Oct 2020 20:20:45: #2 finished! INFO @ Thu, 08 Oct 2020 20:20:45: #2 predicted fragment length is 74 bps INFO @ Thu, 08 Oct 2020 20:20:45: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 08 Oct 2020 20:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_model.r WARNING @ Thu, 08 Oct 2020 20:20:45: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:20:45: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 08 Oct 2020 20:20:45: #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 20:20:45: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:20:48: 2000000 INFO @ Thu, 08 Oct 2020 20:20:52: 7000000 INFO @ Thu, 08 Oct 2020 20:20:55: 3000000 INFO @ Thu, 08 Oct 2020 20:20:59: 8000000 INFO @ Thu, 08 Oct 2020 20:21:02: 4000000 INFO @ Thu, 08 Oct 2020 20:21:06: 9000000 INFO @ Thu, 08 Oct 2020 20:21:08: 5000000 INFO @ Thu, 08 Oct 2020 20:21:10: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:21:13: 10000000 INFO @ Thu, 08 Oct 2020 20:21:15: 6000000 INFO @ Thu, 08 Oct 2020 20:21:20: 11000000 INFO @ Thu, 08 Oct 2020 20:21:22: 7000000 INFO @ Thu, 08 Oct 2020 20:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_summits.bed INFO @ Thu, 08 Oct 2020 20:21:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7168 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:21:27: 12000000 INFO @ Thu, 08 Oct 2020 20:21:29: 8000000 INFO @ Thu, 08 Oct 2020 20:21:30: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:21:30: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:21:30: #1 total tags in treatment: 12421722 INFO @ Thu, 08 Oct 2020 20:21:30: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:21:30: #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 20:21:30: #1 tags after filtering in treatment: 12421722 INFO @ Thu, 08 Oct 2020 20:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:21:30: #1 finished! INFO @ Thu, 08 Oct 2020 20:21:30: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:21:31: #2 number of paired peaks: 261 WARNING @ Thu, 08 Oct 2020 20:21:31: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Thu, 08 Oct 2020 20:21:31: start model_add_line... INFO @ Thu, 08 Oct 2020 20:21:31: start X-correlation... INFO @ Thu, 08 Oct 2020 20:21:31: end of X-cor INFO @ Thu, 08 Oct 2020 20:21:31: #2 finished! INFO @ Thu, 08 Oct 2020 20:21:31: #2 predicted fragment length is 74 bps INFO @ Thu, 08 Oct 2020 20:21:31: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 08 Oct 2020 20:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_model.r WARNING @ Thu, 08 Oct 2020 20:21:31: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:21:31: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 08 Oct 2020 20:21:31: #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 20:21:31: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:21:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:21:36: 9000000 INFO @ Thu, 08 Oct 2020 20:21:43: 10000000 INFO @ Thu, 08 Oct 2020 20:21:50: 11000000 INFO @ Thu, 08 Oct 2020 20:21:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:21:57: 12000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:22:00: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:22:00: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:22:00: #1 total tags in treatment: 12421722 INFO @ Thu, 08 Oct 2020 20:22:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:00: #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 20:22:00: #1 tags after filtering in treatment: 12421722 INFO @ Thu, 08 Oct 2020 20:22:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:00: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:01: #2 number of paired peaks: 261 WARNING @ Thu, 08 Oct 2020 20:22:01: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Thu, 08 Oct 2020 20:22:01: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:01: #2 predicted fragment length is 74 bps INFO @ Thu, 08 Oct 2020 20:22:01: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 08 Oct 2020 20:22:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_model.r WARNING @ Thu, 08 Oct 2020 20:22:01: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:22:01: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 08 Oct 2020 20:22:01: #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 20:22:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:22:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_summits.bed INFO @ Thu, 08 Oct 2020 20:22:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2681 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:22:26: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_summits.bed INFO @ Thu, 08 Oct 2020 20:22:38: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1054 records, 4 fields): 3 millis CompletedMACS2peakCalling