Job ID = 14170120 SRX = SRX8556377 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9221078 spots for SRR12024933/SRR12024933.sra Written 9221078 spots for SRR12024933/SRR12024933.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170720 ("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: 00:30:57 9221078 reads; of these: 9221078 (100.00%) were paired; of these: 5901767 (64.00%) aligned concordantly 0 times 1671174 (18.12%) aligned concordantly exactly 1 time 1648137 (17.87%) aligned concordantly >1 times ---- 5901767 pairs aligned concordantly 0 times; of these: 443342 (7.51%) aligned discordantly 1 time ---- 5458425 pairs aligned 0 times concordantly or discordantly; of these: 10916850 mates make up the pairs; of these: 9208072 (84.35%) aligned 0 times 595586 (5.46%) aligned exactly 1 time 1113192 (10.20%) aligned >1 times 50.07% overall alignment rate Time searching: 00:30:57 Overall time: 00:30:57 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 933273 / 3679123 = 0.2537 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 @ Sat, 11 Dec 2021 06:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.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, 11 Dec 2021 06:12:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:12:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:12:20: 1000000 INFO @ Sat, 11 Dec 2021 06:12:27: 2000000 INFO @ Sat, 11 Dec 2021 06:12:34: 3000000 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 @ Sat, 11 Dec 2021 06:12:41: 4000000 INFO @ Sat, 11 Dec 2021 06:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.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, 11 Dec 2021 06:12:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:12:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:12:49: 5000000 INFO @ Sat, 11 Dec 2021 06:12:50: 1000000 INFO @ Sat, 11 Dec 2021 06:12:57: 6000000 INFO @ Sat, 11 Dec 2021 06:12:58: 2000000 INFO @ Sat, 11 Dec 2021 06:13:04: 7000000 INFO @ Sat, 11 Dec 2021 06:13:06: 3000000 INFO @ Sat, 11 Dec 2021 06:13:07: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:13:07: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:13:07: #1 total tags in treatment: 2451648 INFO @ Sat, 11 Dec 2021 06:13:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:13:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:13:07: #1 tags after filtering in treatment: 2080505 INFO @ Sat, 11 Dec 2021 06:13:07: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 06:13:07: #1 finished! INFO @ Sat, 11 Dec 2021 06:13:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:13:08: #2 number of paired peaks: 3413 INFO @ Sat, 11 Dec 2021 06:13:08: start model_add_line... INFO @ Sat, 11 Dec 2021 06:13:08: start X-correlation... INFO @ Sat, 11 Dec 2021 06:13:08: end of X-cor INFO @ Sat, 11 Dec 2021 06:13:08: #2 finished! INFO @ Sat, 11 Dec 2021 06:13:08: #2 predicted fragment length is 186 bps INFO @ Sat, 11 Dec 2021 06:13:08: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 11 Dec 2021 06:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.05_model.r WARNING @ Sat, 11 Dec 2021 06:13:08: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:13:08: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Sat, 11 Dec 2021 06:13:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:13:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:13:08: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 11 Dec 2021 06:13:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.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, 11 Dec 2021 06:13:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:13:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:13:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:13:13: 4000000 INFO @ Sat, 11 Dec 2021 06:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.05_summits.bed INFO @ Sat, 11 Dec 2021 06:13:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8233 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:13:21: 5000000 INFO @ Sat, 11 Dec 2021 06:13:23: 1000000 INFO @ Sat, 11 Dec 2021 06:13:30: 6000000 INFO @ Sat, 11 Dec 2021 06:13:32: 2000000 INFO @ Sat, 11 Dec 2021 06:13:38: 7000000 INFO @ Sat, 11 Dec 2021 06:13:41: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:13:41: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:13:41: #1 total tags in treatment: 2451648 INFO @ Sat, 11 Dec 2021 06:13:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:13:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:13:41: #1 tags after filtering in treatment: 2080505 INFO @ Sat, 11 Dec 2021 06:13:41: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 06:13:41: #1 finished! INFO @ Sat, 11 Dec 2021 06:13:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:13:41: #2 number of paired peaks: 3413 INFO @ Sat, 11 Dec 2021 06:13:41: start model_add_line... INFO @ Sat, 11 Dec 2021 06:13:41: start X-correlation... INFO @ Sat, 11 Dec 2021 06:13:41: end of X-cor INFO @ Sat, 11 Dec 2021 06:13:41: #2 finished! INFO @ Sat, 11 Dec 2021 06:13:41: #2 predicted fragment length is 186 bps INFO @ Sat, 11 Dec 2021 06:13:41: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 11 Dec 2021 06:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.10_model.r WARNING @ Sat, 11 Dec 2021 06:13:41: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:13:41: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Sat, 11 Dec 2021 06:13:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:13:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:13:42: 3000000 INFO @ Sat, 11 Dec 2021 06:13:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.10_summits.bed INFO @ Sat, 11 Dec 2021 06:13:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2590 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:13:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:14:01: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:14:11: 6000000 INFO @ Sat, 11 Dec 2021 06:14:20: 7000000 INFO @ Sat, 11 Dec 2021 06:14:23: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:14:23: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:14:23: #1 total tags in treatment: 2451648 INFO @ Sat, 11 Dec 2021 06:14:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:14:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:14:23: #1 tags after filtering in treatment: 2080505 INFO @ Sat, 11 Dec 2021 06:14:23: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 11 Dec 2021 06:14:23: #1 finished! INFO @ Sat, 11 Dec 2021 06:14:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:14:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:14:24: #2 number of paired peaks: 3413 INFO @ Sat, 11 Dec 2021 06:14:24: start model_add_line... INFO @ Sat, 11 Dec 2021 06:14:24: start X-correlation... INFO @ Sat, 11 Dec 2021 06:14:24: end of X-cor INFO @ Sat, 11 Dec 2021 06:14:24: #2 finished! INFO @ Sat, 11 Dec 2021 06:14:24: #2 predicted fragment length is 186 bps INFO @ Sat, 11 Dec 2021 06:14:24: #2 alternative fragment length(s) may be 186 bps INFO @ Sat, 11 Dec 2021 06:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.20_model.r WARNING @ Sat, 11 Dec 2021 06:14:24: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:14:24: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Sat, 11 Dec 2021 06:14:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:14:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:14:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:14:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:14:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:14:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556377/SRX8556377.20_summits.bed INFO @ Sat, 11 Dec 2021 06:14:31: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (716 records, 4 fields): 3 millis CompletedMACS2peakCalling