Job ID = 14167187 SRX = SRX9090278 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18819846 spots for SRR12606611/SRR12606611.sra Written 18819846 spots for SRR12606611/SRR12606611.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167720 ("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: 00:05:47 18819846 reads; of these: 18819846 (100.00%) were unpaired; of these: 511370 (2.72%) aligned 0 times 13672925 (72.65%) aligned exactly 1 time 4635551 (24.63%) aligned >1 times 97.28% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 6211916 / 18308476 = 0.3393 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 11:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.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 11:00:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:20: 1000000 INFO @ Fri, 10 Dec 2021 11:00:26: 2000000 INFO @ Fri, 10 Dec 2021 11:00:32: 3000000 INFO @ Fri, 10 Dec 2021 11:00:38: 4000000 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 11:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.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 11:00:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:45: 5000000 INFO @ Fri, 10 Dec 2021 11:00:50: 1000000 INFO @ Fri, 10 Dec 2021 11:00:51: 6000000 INFO @ Fri, 10 Dec 2021 11:00:57: 2000000 INFO @ Fri, 10 Dec 2021 11:00:58: 7000000 INFO @ Fri, 10 Dec 2021 11:01:03: 3000000 INFO @ Fri, 10 Dec 2021 11:01:04: 8000000 INFO @ Fri, 10 Dec 2021 11:01:10: 4000000 INFO @ Fri, 10 Dec 2021 11:01:11: 9000000 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 11:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.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 11:01:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:16: 5000000 INFO @ Fri, 10 Dec 2021 11:01:18: 10000000 INFO @ Fri, 10 Dec 2021 11:01:19: 1000000 INFO @ Fri, 10 Dec 2021 11:01:23: 6000000 INFO @ Fri, 10 Dec 2021 11:01:24: 11000000 INFO @ Fri, 10 Dec 2021 11:01:25: 2000000 INFO @ Fri, 10 Dec 2021 11:01:29: 7000000 INFO @ Fri, 10 Dec 2021 11:01:31: 3000000 INFO @ Fri, 10 Dec 2021 11:01:31: 12000000 INFO @ Fri, 10 Dec 2021 11:01:32: #1 tag size is determined as 49 bps INFO @ Fri, 10 Dec 2021 11:01:32: #1 tag size = 49 INFO @ Fri, 10 Dec 2021 11:01:32: #1 total tags in treatment: 12096560 INFO @ Fri, 10 Dec 2021 11:01:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:01:32: #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 11:01:32: #1 tags after filtering in treatment: 12096560 INFO @ Fri, 10 Dec 2021 11:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:01:32: #1 finished! INFO @ Fri, 10 Dec 2021 11:01:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:01:33: #2 number of paired peaks: 5373 INFO @ Fri, 10 Dec 2021 11:01:33: start model_add_line... INFO @ Fri, 10 Dec 2021 11:01:33: start X-correlation... INFO @ Fri, 10 Dec 2021 11:01:34: end of X-cor INFO @ Fri, 10 Dec 2021 11:01:34: #2 finished! INFO @ Fri, 10 Dec 2021 11:01:34: #2 predicted fragment length is 82 bps INFO @ Fri, 10 Dec 2021 11:01:34: #2 alternative fragment length(s) may be 3,82 bps INFO @ Fri, 10 Dec 2021 11:01:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.05_model.r WARNING @ Fri, 10 Dec 2021 11:01:34: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:01:34: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Fri, 10 Dec 2021 11:01:34: #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 11:01:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:01:35: 8000000 INFO @ Fri, 10 Dec 2021 11:01:36: 4000000 INFO @ Fri, 10 Dec 2021 11:01:42: 9000000 INFO @ Fri, 10 Dec 2021 11:01:42: 5000000 INFO @ Fri, 10 Dec 2021 11:01:48: 6000000 INFO @ Fri, 10 Dec 2021 11:01:48: 10000000 INFO @ Fri, 10 Dec 2021 11:01:53: 7000000 INFO @ Fri, 10 Dec 2021 11:01:54: 11000000 INFO @ Fri, 10 Dec 2021 11:01:59: 8000000 INFO @ Fri, 10 Dec 2021 11:02:01: 12000000 INFO @ Fri, 10 Dec 2021 11:02:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:02: #1 tag size is determined as 49 bps INFO @ Fri, 10 Dec 2021 11:02:02: #1 tag size = 49 INFO @ Fri, 10 Dec 2021 11:02:02: #1 total tags in treatment: 12096560 INFO @ Fri, 10 Dec 2021 11:02:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:02: #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 11:02:02: #1 tags after filtering in treatment: 12096560 INFO @ Fri, 10 Dec 2021 11:02:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:02:02: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:03: #2 number of paired peaks: 5373 INFO @ Fri, 10 Dec 2021 11:02:03: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:03: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:03: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:03: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:03: #2 predicted fragment length is 82 bps INFO @ Fri, 10 Dec 2021 11:02:03: #2 alternative fragment length(s) may be 3,82 bps INFO @ Fri, 10 Dec 2021 11:02:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.10_model.r WARNING @ Fri, 10 Dec 2021 11:02:03: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:03: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Fri, 10 Dec 2021 11:02:03: #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 11:02:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:02:05: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:02:10: 10000000 INFO @ Fri, 10 Dec 2021 11:02:15: 11000000 INFO @ Fri, 10 Dec 2021 11:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.05_summits.bed INFO @ Fri, 10 Dec 2021 11:02:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6812 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:02:20: 12000000 INFO @ Fri, 10 Dec 2021 11:02:20: #1 tag size is determined as 49 bps INFO @ Fri, 10 Dec 2021 11:02:20: #1 tag size = 49 INFO @ Fri, 10 Dec 2021 11:02:20: #1 total tags in treatment: 12096560 INFO @ Fri, 10 Dec 2021 11:02:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:20: #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 11:02:21: #1 tags after filtering in treatment: 12096560 INFO @ Fri, 10 Dec 2021 11:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:02:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:22: #2 number of paired peaks: 5373 INFO @ Fri, 10 Dec 2021 11:02:22: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:22: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:22: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:22: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:22: #2 predicted fragment length is 82 bps INFO @ Fri, 10 Dec 2021 11:02:22: #2 alternative fragment length(s) may be 3,82 bps INFO @ Fri, 10 Dec 2021 11:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.20_model.r WARNING @ Fri, 10 Dec 2021 11:02:22: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:22: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Fri, 10 Dec 2021 11:02:22: #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 11:02:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:02:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.10_summits.bed INFO @ Fri, 10 Dec 2021 11:02:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3895 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:03:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:03:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:03:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9090278/SRX9090278.20_summits.bed INFO @ Fri, 10 Dec 2021 11:03:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1803 records, 4 fields): 5 millis CompletedMACS2peakCalling