Job ID = 6627022 SRX = SRX8325348 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11252830 spots for SRR11772154/SRR11772154.sra Written 11252830 spots for SRR11772154/SRR11772154.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627328 ("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: 00:44:01 11252830 reads; of these: 11252830 (100.00%) were paired; of these: 3222471 (28.64%) aligned concordantly 0 times 4908712 (43.62%) aligned concordantly exactly 1 time 3121647 (27.74%) aligned concordantly >1 times ---- 3222471 pairs aligned concordantly 0 times; of these: 958862 (29.76%) aligned discordantly 1 time ---- 2263609 pairs aligned 0 times concordantly or discordantly; of these: 4527218 mates make up the pairs; of these: 2286826 (50.51%) aligned 0 times 967088 (21.36%) aligned exactly 1 time 1273304 (28.13%) aligned >1 times 89.84% overall alignment rate Time searching: 00:44:01 Overall time: 00:44:01 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 16 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] 5003504 / 8610340 = 0.5811 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 @ Tue, 14 Jul 2020 10:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.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 @ Tue, 14 Jul 2020 10:19:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:19:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:19:25: 1000000 INFO @ Tue, 14 Jul 2020 10:19:32: 2000000 INFO @ Tue, 14 Jul 2020 10:19:38: 3000000 INFO @ Tue, 14 Jul 2020 10:19:45: 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 @ Tue, 14 Jul 2020 10:19:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.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 @ Tue, 14 Jul 2020 10:19:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:19:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:19:51: 5000000 INFO @ Tue, 14 Jul 2020 10:19:55: 1000000 INFO @ Tue, 14 Jul 2020 10:19:58: 6000000 INFO @ Tue, 14 Jul 2020 10:20:02: 2000000 INFO @ Tue, 14 Jul 2020 10:20:04: 7000000 INFO @ Tue, 14 Jul 2020 10:20:09: 3000000 INFO @ Tue, 14 Jul 2020 10:20:11: 8000000 INFO @ Tue, 14 Jul 2020 10:20:15: 4000000 BedGraph に変換中... 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 @ Tue, 14 Jul 2020 10:20:18: 9000000 INFO @ Tue, 14 Jul 2020 10:20:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.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 @ Tue, 14 Jul 2020 10:20:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:22: 5000000 INFO @ Tue, 14 Jul 2020 10:20:25: 10000000 INFO @ Tue, 14 Jul 2020 10:20:25: 1000000 INFO @ Tue, 14 Jul 2020 10:20:26: #1 tag size is determined as 140 bps INFO @ Tue, 14 Jul 2020 10:20:26: #1 tag size = 140 INFO @ Tue, 14 Jul 2020 10:20:26: #1 total tags in treatment: 3517531 INFO @ Tue, 14 Jul 2020 10:20:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:20:26: #1 tags after filtering in treatment: 2913084 INFO @ Tue, 14 Jul 2020 10:20:26: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 14 Jul 2020 10:20:26: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:27: #2 number of paired peaks: 2880 INFO @ Tue, 14 Jul 2020 10:20:27: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:27: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:27: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:27: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:27: #2 predicted fragment length is 229 bps INFO @ Tue, 14 Jul 2020 10:20:27: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 14 Jul 2020 10:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.05_model.r WARNING @ Tue, 14 Jul 2020 10:20:27: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:20:27: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 14 Jul 2020 10:20:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:20:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:29: 6000000 INFO @ Tue, 14 Jul 2020 10:20:32: 2000000 INFO @ Tue, 14 Jul 2020 10:20:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:20:35: 7000000 INFO @ Tue, 14 Jul 2020 10:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.05_summits.bed INFO @ Tue, 14 Jul 2020 10:20:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8666 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:20:39: 3000000 INFO @ Tue, 14 Jul 2020 10:20:42: 8000000 INFO @ Tue, 14 Jul 2020 10:20:45: 4000000 INFO @ Tue, 14 Jul 2020 10:20:49: 9000000 INFO @ Tue, 14 Jul 2020 10:20:52: 5000000 INFO @ Tue, 14 Jul 2020 10:20:56: 10000000 INFO @ Tue, 14 Jul 2020 10:20:57: #1 tag size is determined as 140 bps INFO @ Tue, 14 Jul 2020 10:20:57: #1 tag size = 140 INFO @ Tue, 14 Jul 2020 10:20:57: #1 total tags in treatment: 3517531 INFO @ Tue, 14 Jul 2020 10:20:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:20:57: #1 tags after filtering in treatment: 2913084 INFO @ Tue, 14 Jul 2020 10:20:57: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 14 Jul 2020 10:20:57: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:57: #2 number of paired peaks: 2880 INFO @ Tue, 14 Jul 2020 10:20:57: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:57: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:57: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:57: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:57: #2 predicted fragment length is 229 bps INFO @ Tue, 14 Jul 2020 10:20:57: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 14 Jul 2020 10:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.10_model.r WARNING @ Tue, 14 Jul 2020 10:20:57: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:20:57: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 14 Jul 2020 10:20:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:20:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:59: 6000000 INFO @ Tue, 14 Jul 2020 10:21:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:05: 7000000 INFO @ Tue, 14 Jul 2020 10:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.10_summits.bed INFO @ Tue, 14 Jul 2020 10:21:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3783 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:21:11: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:21:18: 9000000 INFO @ Tue, 14 Jul 2020 10:21:24: 10000000 INFO @ Tue, 14 Jul 2020 10:21:26: #1 tag size is determined as 140 bps INFO @ Tue, 14 Jul 2020 10:21:26: #1 tag size = 140 INFO @ Tue, 14 Jul 2020 10:21:26: #1 total tags in treatment: 3517531 INFO @ Tue, 14 Jul 2020 10:21:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:21:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:21:26: #1 tags after filtering in treatment: 2913084 INFO @ Tue, 14 Jul 2020 10:21:26: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 14 Jul 2020 10:21:26: #1 finished! INFO @ Tue, 14 Jul 2020 10:21:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:21:26: #2 number of paired peaks: 2880 INFO @ Tue, 14 Jul 2020 10:21:26: start model_add_line... INFO @ Tue, 14 Jul 2020 10:21:26: start X-correlation... INFO @ Tue, 14 Jul 2020 10:21:26: end of X-cor INFO @ Tue, 14 Jul 2020 10:21:26: #2 finished! INFO @ Tue, 14 Jul 2020 10:21:26: #2 predicted fragment length is 229 bps INFO @ Tue, 14 Jul 2020 10:21:26: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 14 Jul 2020 10:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.20_model.r WARNING @ Tue, 14 Jul 2020 10:21:26: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:21:26: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 14 Jul 2020 10:21:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:21:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:21:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:21:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325348/SRX8325348.20_summits.bed INFO @ Tue, 14 Jul 2020 10:21:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1206 records, 4 fields): 2 millis CompletedMACS2peakCalling