Job ID = 14168336 SRX = ERX3978851 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29172710 spots for ERR3975920/ERR3975920.sra Written 29172710 spots for ERR3975920/ERR3975920.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169664 ("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: 01:30:29 29172710 reads; of these: 29172710 (100.00%) were paired; of these: 10114478 (34.67%) aligned concordantly 0 times 14772656 (50.64%) aligned concordantly exactly 1 time 4285576 (14.69%) aligned concordantly >1 times ---- 10114478 pairs aligned concordantly 0 times; of these: 829150 (8.20%) aligned discordantly 1 time ---- 9285328 pairs aligned 0 times concordantly or discordantly; of these: 18570656 mates make up the pairs; of these: 9195214 (49.51%) aligned 0 times 5952452 (32.05%) aligned exactly 1 time 3422990 (18.43%) aligned >1 times 84.24% overall alignment rate Time searching: 01:30:29 Overall time: 01:30:29 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 24 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] 14955082 / 19628266 = 0.7619 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 19:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.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 19:20:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:20:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:20:26: 1000000 INFO @ Fri, 10 Dec 2021 19:20:33: 2000000 INFO @ Fri, 10 Dec 2021 19:20:39: 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 19:20:47: 4000000 INFO @ Fri, 10 Dec 2021 19:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.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 19:20:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:20:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:20:55: 5000000 INFO @ Fri, 10 Dec 2021 19:20:57: 1000000 INFO @ Fri, 10 Dec 2021 19:21:03: 6000000 INFO @ Fri, 10 Dec 2021 19:21:05: 2000000 INFO @ Fri, 10 Dec 2021 19:21:10: 7000000 INFO @ Fri, 10 Dec 2021 19:21:13: 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 19:21:18: 8000000 INFO @ Fri, 10 Dec 2021 19:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.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 19:21:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:21:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:21:22: 4000000 INFO @ Fri, 10 Dec 2021 19:21:25: 9000000 INFO @ Fri, 10 Dec 2021 19:21:28: 1000000 INFO @ Fri, 10 Dec 2021 19:21:30: 5000000 INFO @ Fri, 10 Dec 2021 19:21:33: 10000000 INFO @ Fri, 10 Dec 2021 19:21:36: 2000000 INFO @ Fri, 10 Dec 2021 19:21:38: 6000000 INFO @ Fri, 10 Dec 2021 19:21:40: 11000000 INFO @ Fri, 10 Dec 2021 19:21:45: 7000000 INFO @ Fri, 10 Dec 2021 19:21:46: 3000000 INFO @ Fri, 10 Dec 2021 19:21:47: 12000000 INFO @ Fri, 10 Dec 2021 19:21:52: 8000000 INFO @ Fri, 10 Dec 2021 19:21:55: 13000000 INFO @ Fri, 10 Dec 2021 19:21:56: 4000000 INFO @ Fri, 10 Dec 2021 19:22:01: 9000000 INFO @ Fri, 10 Dec 2021 19:22:03: 14000000 INFO @ Fri, 10 Dec 2021 19:22:04: 5000000 INFO @ Fri, 10 Dec 2021 19:22:09: 10000000 INFO @ Fri, 10 Dec 2021 19:22:11: 15000000 INFO @ Fri, 10 Dec 2021 19:22:12: 6000000 INFO @ Fri, 10 Dec 2021 19:22:17: 11000000 INFO @ Fri, 10 Dec 2021 19:22:19: 16000000 INFO @ Fri, 10 Dec 2021 19:22:21: 7000000 INFO @ Fri, 10 Dec 2021 19:22:24: 12000000 INFO @ Fri, 10 Dec 2021 19:22:26: 17000000 INFO @ Fri, 10 Dec 2021 19:22:31: 8000000 INFO @ Fri, 10 Dec 2021 19:22:32: 13000000 INFO @ Fri, 10 Dec 2021 19:22:33: 18000000 INFO @ Fri, 10 Dec 2021 19:22:40: 14000000 INFO @ Fri, 10 Dec 2021 19:22:41: 9000000 INFO @ Fri, 10 Dec 2021 19:22:42: 19000000 INFO @ Fri, 10 Dec 2021 19:22:44: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:22:44: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:22:44: #1 total tags in treatment: 4607855 INFO @ Fri, 10 Dec 2021 19:22:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:22:44: #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 19:22:44: #1 tags after filtering in treatment: 4192389 INFO @ Fri, 10 Dec 2021 19:22:44: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 19:22:44: #1 finished! INFO @ Fri, 10 Dec 2021 19:22:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:22:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:22:45: #2 number of paired peaks: 2239 INFO @ Fri, 10 Dec 2021 19:22:45: start model_add_line... INFO @ Fri, 10 Dec 2021 19:22:45: start X-correlation... INFO @ Fri, 10 Dec 2021 19:22:45: end of X-cor INFO @ Fri, 10 Dec 2021 19:22:45: #2 finished! INFO @ Fri, 10 Dec 2021 19:22:45: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 19:22:45: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 19:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.05_model.r WARNING @ Fri, 10 Dec 2021 19:22:45: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:22:45: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 19:22:45: #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 19:22:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:22:48: 15000000 INFO @ Fri, 10 Dec 2021 19:22:48: 10000000 INFO @ Fri, 10 Dec 2021 19:22:55: 16000000 INFO @ Fri, 10 Dec 2021 19:22:56: 11000000 INFO @ Fri, 10 Dec 2021 19:22:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:23:03: 17000000 INFO @ Fri, 10 Dec 2021 19:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.05_summits.bed INFO @ Fri, 10 Dec 2021 19:23:03: Done! INFO @ Fri, 10 Dec 2021 19:23:04: 12000000 pass1 - making usageList (15 chroms): 26 millis pass2 - checking and writing primary data (6146 records, 4 fields): 56 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:23:10: 18000000 INFO @ Fri, 10 Dec 2021 19:23:13: 13000000 INFO @ Fri, 10 Dec 2021 19:23:16: 19000000 INFO @ Fri, 10 Dec 2021 19:23:18: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:23:18: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:23:18: #1 total tags in treatment: 4607855 INFO @ Fri, 10 Dec 2021 19:23:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:18: #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 19:23:18: #1 tags after filtering in treatment: 4192389 INFO @ Fri, 10 Dec 2021 19:23:18: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 19:23:18: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:18: #2 number of paired peaks: 2239 INFO @ Fri, 10 Dec 2021 19:23:18: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:19: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:19: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:19: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:19: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 19:23:19: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 19:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.10_model.r WARNING @ Fri, 10 Dec 2021 19:23:19: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:19: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 19:23:19: #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 19:23:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:23:21: 14000000 INFO @ Fri, 10 Dec 2021 19:23:28: 15000000 INFO @ Fri, 10 Dec 2021 19:23:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.10_summits.bed INFO @ Fri, 10 Dec 2021 19:23:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2661 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:23:35: 16000000 INFO @ Fri, 10 Dec 2021 19:23:41: 17000000 INFO @ Fri, 10 Dec 2021 19:23:48: 18000000 INFO @ Fri, 10 Dec 2021 19:23:54: 19000000 INFO @ Fri, 10 Dec 2021 19:23:56: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:23:56: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:23:56: #1 total tags in treatment: 4607855 INFO @ Fri, 10 Dec 2021 19:23:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:23:56: #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 19:23:56: #1 tags after filtering in treatment: 4192389 INFO @ Fri, 10 Dec 2021 19:23:56: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 19:23:56: #1 finished! INFO @ Fri, 10 Dec 2021 19:23:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:23:56: #2 number of paired peaks: 2239 INFO @ Fri, 10 Dec 2021 19:23:56: start model_add_line... INFO @ Fri, 10 Dec 2021 19:23:56: start X-correlation... INFO @ Fri, 10 Dec 2021 19:23:56: end of X-cor INFO @ Fri, 10 Dec 2021 19:23:56: #2 finished! INFO @ Fri, 10 Dec 2021 19:23:56: #2 predicted fragment length is 149 bps INFO @ Fri, 10 Dec 2021 19:23:56: #2 alternative fragment length(s) may be 149 bps INFO @ Fri, 10 Dec 2021 19:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.20_model.r WARNING @ Fri, 10 Dec 2021 19:23:56: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:23:56: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Fri, 10 Dec 2021 19:23:56: #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 19:23:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:24:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978851/ERX3978851.20_summits.bed INFO @ Fri, 10 Dec 2021 19:24:11: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (909 records, 4 fields): 27 millis CompletedMACS2peakCalling