Job ID = 12264849 SRX = SRX2789127 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27444029 spots for SRR5515770/SRR5515770.sra Written 27444029 spots for SRR5515770/SRR5515770.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265216 ("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: 00:11:38 27444029 reads; of these: 27444029 (100.00%) were paired; of these: 25626594 (93.38%) aligned concordantly 0 times 766843 (2.79%) aligned concordantly exactly 1 time 1050592 (3.83%) aligned concordantly >1 times ---- 25626594 pairs aligned concordantly 0 times; of these: 240542 (0.94%) aligned discordantly 1 time ---- 25386052 pairs aligned 0 times concordantly or discordantly; of these: 50772104 mates make up the pairs; of these: 50209812 (98.89%) aligned 0 times 142675 (0.28%) aligned exactly 1 time 419617 (0.83%) aligned >1 times 8.52% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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_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] 479169 / 2037766 = 0.2351 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 06:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.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 06:10:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:10:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:10:44: 1000000 INFO @ Sat, 03 Apr 2021 06:10:53: 2000000 INFO @ Sat, 03 Apr 2021 06:11:02: 3000000 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 06:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.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 06:11:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:09: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:11:09: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:11:09: #1 total tags in treatment: 1363746 INFO @ Sat, 03 Apr 2021 06:11:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:11:09: #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 06:11:09: #1 tags after filtering in treatment: 948179 INFO @ Sat, 03 Apr 2021 06:11:09: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:11:09: #1 finished! INFO @ Sat, 03 Apr 2021 06:11:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:11:09: #2 number of paired peaks: 2217 INFO @ Sat, 03 Apr 2021 06:11:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:11:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:11:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:11:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:11:09: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 06:11:09: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Apr 2021 06:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.05_model.r WARNING @ Sat, 03 Apr 2021 06:11:09: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:11:09: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 03 Apr 2021 06:11:09: #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 06:11:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:11:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:11:13: 1000000 INFO @ Sat, 03 Apr 2021 06:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.05_summits.bed INFO @ Sat, 03 Apr 2021 06:11:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (958 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:11:21: 2000000 INFO @ Sat, 03 Apr 2021 06:11:28: 3000000 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 06:11:34: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:11:34: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:11:34: #1 total tags in treatment: 1363746 INFO @ Sat, 03 Apr 2021 06:11:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:11:34: #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 06:11:34: #1 tags after filtering in treatment: 948179 INFO @ Sat, 03 Apr 2021 06:11:34: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:11:34: #1 finished! INFO @ Sat, 03 Apr 2021 06:11:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:11:34: #2 number of paired peaks: 2217 INFO @ Sat, 03 Apr 2021 06:11:34: start model_add_line... INFO @ Sat, 03 Apr 2021 06:11:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:11:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:11:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:11:34: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 06:11:34: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Apr 2021 06:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.10_model.r WARNING @ Sat, 03 Apr 2021 06:11:34: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:11:34: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 03 Apr 2021 06:11:34: #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 06:11:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.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 06:11:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:11:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:11:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.10_summits.bed INFO @ Sat, 03 Apr 2021 06:11:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:11:45: 1000000 INFO @ Sat, 03 Apr 2021 06:11:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:12:06: 3000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:12:15: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:12:15: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:12:15: #1 total tags in treatment: 1363746 INFO @ Sat, 03 Apr 2021 06:12:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:12:15: #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 06:12:15: #1 tags after filtering in treatment: 948179 INFO @ Sat, 03 Apr 2021 06:12:15: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:12:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:12:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:12:15: #2 number of paired peaks: 2217 INFO @ Sat, 03 Apr 2021 06:12:15: start model_add_line... INFO @ Sat, 03 Apr 2021 06:12:15: start X-correlation... INFO @ Sat, 03 Apr 2021 06:12:15: end of X-cor INFO @ Sat, 03 Apr 2021 06:12:15: #2 finished! INFO @ Sat, 03 Apr 2021 06:12:15: #2 predicted fragment length is 147 bps INFO @ Sat, 03 Apr 2021 06:12:15: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 03 Apr 2021 06:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.20_model.r WARNING @ Sat, 03 Apr 2021 06:12:15: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:12:15: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 03 Apr 2021 06:12:15: #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 06:12:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:12:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2789127/SRX2789127.20_summits.bed INFO @ Sat, 03 Apr 2021 06:12:20: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis CompletedMACS2peakCalling