Job ID = 12264864 SRX = SRX3032263 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16300043 spots for SRR5863953/SRR5863953.sra Written 16300043 spots for SRR5863953/SRR5863953.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265112 ("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: 00:07:12 16300043 reads; of these: 16300043 (100.00%) were unpaired; of these: 5758632 (35.33%) aligned 0 times 9070030 (55.64%) aligned exactly 1 time 1471381 (9.03%) aligned >1 times 64.67% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 3363508 / 10541411 = 0.3191 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.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, 03 Apr 2021 06:06:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:22: 1000000 INFO @ Sat, 03 Apr 2021 06:06:34: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.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, 03 Apr 2021 06:06:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:06:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:06:46: 3000000 INFO @ Sat, 03 Apr 2021 06:06:54: 1000000 INFO @ Sat, 03 Apr 2021 06:06:58: 4000000 INFO @ Sat, 03 Apr 2021 06:07:07: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.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, 03 Apr 2021 06:07:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:10: 5000000 INFO @ Sat, 03 Apr 2021 06:07:20: 3000000 INFO @ Sat, 03 Apr 2021 06:07:21: 1000000 INFO @ Sat, 03 Apr 2021 06:07:24: 6000000 INFO @ Sat, 03 Apr 2021 06:07:32: 4000000 INFO @ Sat, 03 Apr 2021 06:07:33: 2000000 INFO @ Sat, 03 Apr 2021 06:07:37: 7000000 INFO @ Sat, 03 Apr 2021 06:07:40: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:07:40: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:07:40: #1 total tags in treatment: 7177903 INFO @ Sat, 03 Apr 2021 06:07:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:07:40: #1 tags after filtering in treatment: 7177903 INFO @ Sat, 03 Apr 2021 06:07:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:07:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:41: #2 number of paired peaks: 2869 INFO @ Sat, 03 Apr 2021 06:07:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:41: #2 predicted fragment length is 100 bps INFO @ Sat, 03 Apr 2021 06:07:41: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 03 Apr 2021 06:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.05_model.r WARNING @ Sat, 03 Apr 2021 06:07:41: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:41: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 03 Apr 2021 06:07:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:07:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:07:43: 3000000 INFO @ Sat, 03 Apr 2021 06:07:45: 5000000 INFO @ Sat, 03 Apr 2021 06:07:54: 4000000 INFO @ Sat, 03 Apr 2021 06:07:59: 6000000 INFO @ Sat, 03 Apr 2021 06:08:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:05: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:08:13: 7000000 INFO @ Sat, 03 Apr 2021 06:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.05_summits.bed INFO @ Sat, 03 Apr 2021 06:08:15: Done! INFO @ Sat, 03 Apr 2021 06:08:16: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:08:16: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:08:16: #1 total tags in treatment: 7177903 INFO @ Sat, 03 Apr 2021 06:08:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (13613 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:16: #1 tags after filtering in treatment: 7177903 INFO @ Sat, 03 Apr 2021 06:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:16: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:17: #2 number of paired peaks: 2869 INFO @ Sat, 03 Apr 2021 06:08:17: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:17: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:17: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:17: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:17: #2 predicted fragment length is 100 bps INFO @ Sat, 03 Apr 2021 06:08:17: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 03 Apr 2021 06:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.10_model.r WARNING @ Sat, 03 Apr 2021 06:08:17: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:17: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 03 Apr 2021 06:08:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:08:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:17: 6000000 INFO @ Sat, 03 Apr 2021 06:08:27: 7000000 INFO @ Sat, 03 Apr 2021 06:08:29: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:08:29: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:08:29: #1 total tags in treatment: 7177903 INFO @ Sat, 03 Apr 2021 06:08:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:08:29: #1 tags after filtering in treatment: 7177903 INFO @ Sat, 03 Apr 2021 06:08:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:08:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:30: #2 number of paired peaks: 2869 INFO @ Sat, 03 Apr 2021 06:08:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:30: #2 predicted fragment length is 100 bps INFO @ Sat, 03 Apr 2021 06:08:30: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 03 Apr 2021 06:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.20_model.r WARNING @ Sat, 03 Apr 2021 06:08:30: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:30: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 03 Apr 2021 06:08:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:08:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:08:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.10_summits.bed INFO @ Sat, 03 Apr 2021 06:08:51: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8202 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:09:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:09:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032263/SRX3032263.20_summits.bed INFO @ Sat, 03 Apr 2021 06:09:04: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (3202 records, 4 fields): 6 millis CompletedMACS2peakCalling