Job ID = 14170310 SRX = SRX8556398 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23018267 spots for SRR12024954/SRR12024954.sra Written 23018267 spots for SRR12024954/SRR12024954.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171043 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:25:03 23018267 reads; of these: 23018267 (100.00%) were paired; of these: 13331501 (57.92%) aligned concordantly 0 times 5363985 (23.30%) aligned concordantly exactly 1 time 4322781 (18.78%) aligned concordantly >1 times ---- 13331501 pairs aligned concordantly 0 times; of these: 897316 (6.73%) aligned discordantly 1 time ---- 12434185 pairs aligned 0 times concordantly or discordantly; of these: 24868370 mates make up the pairs; of these: 19215561 (77.27%) aligned 0 times 2962635 (11.91%) aligned exactly 1 time 2690174 (10.82%) aligned >1 times 58.26% overall alignment rate Time searching: 01:25:04 Overall time: 01:25:04 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] 3861778 / 10246070 = 0.3769 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 07:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.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 07:55:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:55:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:55:26: 1000000 INFO @ Sat, 11 Dec 2021 07:55:33: 2000000 INFO @ Sat, 11 Dec 2021 07:55:41: 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 07:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.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 07:55:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:55:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:55:49: 4000000 INFO @ Sat, 11 Dec 2021 07:55:57: 1000000 INFO @ Sat, 11 Dec 2021 07:55:59: 5000000 INFO @ Sat, 11 Dec 2021 07:56:06: 2000000 INFO @ Sat, 11 Dec 2021 07:56:08: 6000000 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 07:56:16: 3000000 INFO @ Sat, 11 Dec 2021 07:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.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 07:56:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:56:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:56:18: 7000000 INFO @ Sat, 11 Dec 2021 07:56:26: 4000000 INFO @ Sat, 11 Dec 2021 07:56:27: 1000000 INFO @ Sat, 11 Dec 2021 07:56:27: 8000000 INFO @ Sat, 11 Dec 2021 07:56:35: 5000000 INFO @ Sat, 11 Dec 2021 07:56:36: 2000000 INFO @ Sat, 11 Dec 2021 07:56:37: 9000000 INFO @ Sat, 11 Dec 2021 07:56:45: 6000000 INFO @ Sat, 11 Dec 2021 07:56:46: 3000000 INFO @ Sat, 11 Dec 2021 07:56:46: 10000000 INFO @ Sat, 11 Dec 2021 07:56:54: 7000000 INFO @ Sat, 11 Dec 2021 07:56:55: 4000000 INFO @ Sat, 11 Dec 2021 07:56:56: 11000000 INFO @ Sat, 11 Dec 2021 07:57:04: 8000000 INFO @ Sat, 11 Dec 2021 07:57:05: 5000000 INFO @ Sat, 11 Dec 2021 07:57:06: 12000000 INFO @ Sat, 11 Dec 2021 07:57:13: 9000000 INFO @ Sat, 11 Dec 2021 07:57:15: 6000000 INFO @ Sat, 11 Dec 2021 07:57:15: 13000000 INFO @ Sat, 11 Dec 2021 07:57:23: 10000000 INFO @ Sat, 11 Dec 2021 07:57:24: 7000000 INFO @ Sat, 11 Dec 2021 07:57:25: 14000000 INFO @ Sat, 11 Dec 2021 07:57:32: 11000000 INFO @ Sat, 11 Dec 2021 07:57:34: 8000000 INFO @ Sat, 11 Dec 2021 07:57:34: 15000000 INFO @ Sat, 11 Dec 2021 07:57:42: 12000000 INFO @ Sat, 11 Dec 2021 07:57:44: 9000000 INFO @ Sat, 11 Dec 2021 07:57:44: 16000000 INFO @ Sat, 11 Dec 2021 07:57:52: 13000000 INFO @ Sat, 11 Dec 2021 07:57:53: 10000000 INFO @ Sat, 11 Dec 2021 07:57:53: 17000000 INFO @ Sat, 11 Dec 2021 07:58:01: 14000000 INFO @ Sat, 11 Dec 2021 07:58:03: 18000000 INFO @ Sat, 11 Dec 2021 07:58:03: 11000000 INFO @ Sat, 11 Dec 2021 07:58:10: 15000000 INFO @ Sat, 11 Dec 2021 07:58:12: 19000000 INFO @ Sat, 11 Dec 2021 07:58:13: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:58:13: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:58:13: #1 total tags in treatment: 5979839 INFO @ Sat, 11 Dec 2021 07:58:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:58:13: #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 07:58:13: #1 tags after filtering in treatment: 4966384 INFO @ Sat, 11 Dec 2021 07:58:13: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 07:58:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:58:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:58:13: 12000000 INFO @ Sat, 11 Dec 2021 07:58:13: #2 number of paired peaks: 2802 INFO @ Sat, 11 Dec 2021 07:58:13: start model_add_line... INFO @ Sat, 11 Dec 2021 07:58:13: start X-correlation... INFO @ Sat, 11 Dec 2021 07:58:13: end of X-cor INFO @ Sat, 11 Dec 2021 07:58:13: #2 finished! INFO @ Sat, 11 Dec 2021 07:58:13: #2 predicted fragment length is 197 bps INFO @ Sat, 11 Dec 2021 07:58:13: #2 alternative fragment length(s) may be 197 bps INFO @ Sat, 11 Dec 2021 07:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.05_model.r WARNING @ Sat, 11 Dec 2021 07:58:13: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:58:13: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Sat, 11 Dec 2021 07:58:13: #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 07:58:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:58:20: 16000000 INFO @ Sat, 11 Dec 2021 07:58:23: 13000000 INFO @ Sat, 11 Dec 2021 07:58:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:58:29: 17000000 INFO @ Sat, 11 Dec 2021 07:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.05_summits.bed INFO @ Sat, 11 Dec 2021 07:58:31: Done! INFO @ Sat, 11 Dec 2021 07:58:32: 14000000 pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12776 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:58:38: 18000000 INFO @ Sat, 11 Dec 2021 07:58:42: 15000000 INFO @ Sat, 11 Dec 2021 07:58:48: 19000000 INFO @ Sat, 11 Dec 2021 07:58:48: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:58:48: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:58:48: #1 total tags in treatment: 5979839 INFO @ Sat, 11 Dec 2021 07:58:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:58:48: #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 07:58:49: #1 tags after filtering in treatment: 4966384 INFO @ Sat, 11 Dec 2021 07:58:49: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 07:58:49: #1 finished! INFO @ Sat, 11 Dec 2021 07:58:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:58:49: #2 number of paired peaks: 2802 INFO @ Sat, 11 Dec 2021 07:58:49: start model_add_line... INFO @ Sat, 11 Dec 2021 07:58:49: start X-correlation... INFO @ Sat, 11 Dec 2021 07:58:49: end of X-cor INFO @ Sat, 11 Dec 2021 07:58:49: #2 finished! INFO @ Sat, 11 Dec 2021 07:58:49: #2 predicted fragment length is 197 bps INFO @ Sat, 11 Dec 2021 07:58:49: #2 alternative fragment length(s) may be 197 bps INFO @ Sat, 11 Dec 2021 07:58:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.10_model.r WARNING @ Sat, 11 Dec 2021 07:58:49: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:58:49: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Sat, 11 Dec 2021 07:58:49: #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 07:58:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:58:52: 16000000 INFO @ Sat, 11 Dec 2021 07:59:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:59:01: 17000000 INFO @ Sat, 11 Dec 2021 07:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:59:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.10_summits.bed INFO @ Sat, 11 Dec 2021 07:59:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7929 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:59:09: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:59:17: 19000000 INFO @ Sat, 11 Dec 2021 07:59:18: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:59:18: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:59:18: #1 total tags in treatment: 5979839 INFO @ Sat, 11 Dec 2021 07:59:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:59:18: #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 07:59:18: #1 tags after filtering in treatment: 4966384 INFO @ Sat, 11 Dec 2021 07:59:18: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 07:59:18: #1 finished! INFO @ Sat, 11 Dec 2021 07:59:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:59:19: #2 number of paired peaks: 2802 INFO @ Sat, 11 Dec 2021 07:59:19: start model_add_line... INFO @ Sat, 11 Dec 2021 07:59:19: start X-correlation... INFO @ Sat, 11 Dec 2021 07:59:19: end of X-cor INFO @ Sat, 11 Dec 2021 07:59:19: #2 finished! INFO @ Sat, 11 Dec 2021 07:59:19: #2 predicted fragment length is 197 bps INFO @ Sat, 11 Dec 2021 07:59:19: #2 alternative fragment length(s) may be 197 bps INFO @ Sat, 11 Dec 2021 07:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.20_model.r WARNING @ Sat, 11 Dec 2021 07:59:19: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:59:19: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Sat, 11 Dec 2021 07:59:19: #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 07:59:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:59:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556398/SRX8556398.20_summits.bed INFO @ Sat, 11 Dec 2021 07:59:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3623 records, 4 fields): 4 millis CompletedMACS2peakCalling