Job ID = 14168302 SRX = SRX9263545 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25360592 spots for SRR12794425/SRR12794425.sra Written 25360592 spots for SRR12794425/SRR12794425.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169506 ("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: 00:48:59 25360592 reads; of these: 25360592 (100.00%) were paired; of these: 17110968 (67.47%) aligned concordantly 0 times 5510782 (21.73%) aligned concordantly exactly 1 time 2738842 (10.80%) aligned concordantly >1 times ---- 17110968 pairs aligned concordantly 0 times; of these: 2516128 (14.70%) aligned discordantly 1 time ---- 14594840 pairs aligned 0 times concordantly or discordantly; of these: 29189680 mates make up the pairs; of these: 26238890 (89.89%) aligned 0 times 684069 (2.34%) aligned exactly 1 time 2266721 (7.77%) aligned >1 times 48.27% overall alignment rate Time searching: 00:48:59 Overall time: 00:48:59 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 20 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] 1451578 / 10666690 = 0.1361 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 18:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.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 18:14:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:14:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:15:03: 1000000 INFO @ Fri, 10 Dec 2021 18:15:11: 2000000 INFO @ Fri, 10 Dec 2021 18:15:19: 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 @ Fri, 10 Dec 2021 18:15:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.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 18:15:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:15:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:15:27: 4000000 INFO @ Fri, 10 Dec 2021 18:15:35: 1000000 INFO @ Fri, 10 Dec 2021 18:15:36: 5000000 INFO @ Fri, 10 Dec 2021 18:15:44: 2000000 INFO @ Fri, 10 Dec 2021 18:15:45: 6000000 INFO @ Fri, 10 Dec 2021 18:15:53: 3000000 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 18:15:54: 7000000 INFO @ Fri, 10 Dec 2021 18:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.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 18:15:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:15:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:16:02: 4000000 INFO @ Fri, 10 Dec 2021 18:16:04: 8000000 INFO @ Fri, 10 Dec 2021 18:16:05: 1000000 INFO @ Fri, 10 Dec 2021 18:16:11: 5000000 INFO @ Fri, 10 Dec 2021 18:16:13: 9000000 INFO @ Fri, 10 Dec 2021 18:16:14: 2000000 INFO @ Fri, 10 Dec 2021 18:16:20: 6000000 INFO @ Fri, 10 Dec 2021 18:16:22: 10000000 INFO @ Fri, 10 Dec 2021 18:16:23: 3000000 INFO @ Fri, 10 Dec 2021 18:16:29: 7000000 INFO @ Fri, 10 Dec 2021 18:16:31: 11000000 INFO @ Fri, 10 Dec 2021 18:16:32: 4000000 INFO @ Fri, 10 Dec 2021 18:16:38: 8000000 INFO @ Fri, 10 Dec 2021 18:16:40: 12000000 INFO @ Fri, 10 Dec 2021 18:16:41: 5000000 INFO @ Fri, 10 Dec 2021 18:16:48: 9000000 INFO @ Fri, 10 Dec 2021 18:16:49: 13000000 INFO @ Fri, 10 Dec 2021 18:16:50: 6000000 INFO @ Fri, 10 Dec 2021 18:16:57: 10000000 INFO @ Fri, 10 Dec 2021 18:16:59: 14000000 INFO @ Fri, 10 Dec 2021 18:17:00: 7000000 INFO @ Fri, 10 Dec 2021 18:17:06: 11000000 INFO @ Fri, 10 Dec 2021 18:17:08: 15000000 INFO @ Fri, 10 Dec 2021 18:17:09: 8000000 INFO @ Fri, 10 Dec 2021 18:17:15: 12000000 INFO @ Fri, 10 Dec 2021 18:17:17: 16000000 INFO @ Fri, 10 Dec 2021 18:17:18: 9000000 INFO @ Fri, 10 Dec 2021 18:17:24: 13000000 INFO @ Fri, 10 Dec 2021 18:17:26: 17000000 INFO @ Fri, 10 Dec 2021 18:17:27: 10000000 INFO @ Fri, 10 Dec 2021 18:17:34: 14000000 INFO @ Fri, 10 Dec 2021 18:17:35: 18000000 INFO @ Fri, 10 Dec 2021 18:17:36: 11000000 INFO @ Fri, 10 Dec 2021 18:17:43: 15000000 INFO @ Fri, 10 Dec 2021 18:17:45: 19000000 INFO @ Fri, 10 Dec 2021 18:17:46: 12000000 INFO @ Fri, 10 Dec 2021 18:17:52: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:17:54: 20000000 INFO @ Fri, 10 Dec 2021 18:17:55: 13000000 INFO @ Fri, 10 Dec 2021 18:18:01: 17000000 INFO @ Fri, 10 Dec 2021 18:18:04: 21000000 INFO @ Fri, 10 Dec 2021 18:18:05: 14000000 INFO @ Fri, 10 Dec 2021 18:18:09: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 18:18:09: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 18:18:09: #1 total tags in treatment: 6972646 INFO @ Fri, 10 Dec 2021 18:18:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:18:09: #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 18:18:10: #1 tags after filtering in treatment: 5623900 INFO @ Fri, 10 Dec 2021 18:18:10: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 18:18:10: #1 finished! INFO @ Fri, 10 Dec 2021 18:18:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:18:10: #2 number of paired peaks: 1859 INFO @ Fri, 10 Dec 2021 18:18:10: start model_add_line... INFO @ Fri, 10 Dec 2021 18:18:10: start X-correlation... INFO @ Fri, 10 Dec 2021 18:18:10: end of X-cor INFO @ Fri, 10 Dec 2021 18:18:10: #2 finished! INFO @ Fri, 10 Dec 2021 18:18:10: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Dec 2021 18:18:10: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Dec 2021 18:18:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.05_model.r WARNING @ Fri, 10 Dec 2021 18:18:10: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:18:10: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Fri, 10 Dec 2021 18:18:10: #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 18:18:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:18:11: 18000000 INFO @ Fri, 10 Dec 2021 18:18:14: 15000000 INFO @ Fri, 10 Dec 2021 18:18:20: 19000000 INFO @ Fri, 10 Dec 2021 18:18:23: 16000000 INFO @ Fri, 10 Dec 2021 18:18:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:18:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:18:30: 20000000 INFO @ Fri, 10 Dec 2021 18:18:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.05_summits.bed INFO @ Fri, 10 Dec 2021 18:18:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4879 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:18:32: 17000000 INFO @ Fri, 10 Dec 2021 18:18:39: 21000000 INFO @ Fri, 10 Dec 2021 18:18:41: 18000000 INFO @ Fri, 10 Dec 2021 18:18:44: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 18:18:44: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 18:18:44: #1 total tags in treatment: 6972646 INFO @ Fri, 10 Dec 2021 18:18:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:18:44: #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 18:18:44: #1 tags after filtering in treatment: 5623900 INFO @ Fri, 10 Dec 2021 18:18:44: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 18:18:44: #1 finished! INFO @ Fri, 10 Dec 2021 18:18:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:18:45: #2 number of paired peaks: 1859 INFO @ Fri, 10 Dec 2021 18:18:45: start model_add_line... INFO @ Fri, 10 Dec 2021 18:18:45: start X-correlation... INFO @ Fri, 10 Dec 2021 18:18:45: end of X-cor INFO @ Fri, 10 Dec 2021 18:18:45: #2 finished! INFO @ Fri, 10 Dec 2021 18:18:45: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Dec 2021 18:18:45: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Dec 2021 18:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.10_model.r WARNING @ Fri, 10 Dec 2021 18:18:45: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:18:45: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Fri, 10 Dec 2021 18:18:45: #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 18:18:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:18:50: 19000000 INFO @ Fri, 10 Dec 2021 18:18:57: 20000000 INFO @ Fri, 10 Dec 2021 18:18:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.10_summits.bed INFO @ Fri, 10 Dec 2021 18:19:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2457 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:19:05: 21000000 INFO @ Fri, 10 Dec 2021 18:19:09: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 18:19:09: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 18:19:09: #1 total tags in treatment: 6972646 INFO @ Fri, 10 Dec 2021 18:19:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:19:09: #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 18:19:09: #1 tags after filtering in treatment: 5623900 INFO @ Fri, 10 Dec 2021 18:19:09: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 18:19:09: #1 finished! INFO @ Fri, 10 Dec 2021 18:19:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:19:10: #2 number of paired peaks: 1859 INFO @ Fri, 10 Dec 2021 18:19:10: start model_add_line... INFO @ Fri, 10 Dec 2021 18:19:10: start X-correlation... INFO @ Fri, 10 Dec 2021 18:19:10: end of X-cor INFO @ Fri, 10 Dec 2021 18:19:10: #2 finished! INFO @ Fri, 10 Dec 2021 18:19:10: #2 predicted fragment length is 195 bps INFO @ Fri, 10 Dec 2021 18:19:10: #2 alternative fragment length(s) may be 195 bps INFO @ Fri, 10 Dec 2021 18:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.20_model.r WARNING @ Fri, 10 Dec 2021 18:19:10: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:19:10: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Fri, 10 Dec 2021 18:19:10: #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 18:19:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:19:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263545/SRX9263545.20_summits.bed INFO @ Fri, 10 Dec 2021 18:19:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (983 records, 4 fields): 3 millis CompletedMACS2peakCalling