Job ID = 14168329 SRX = ERX3978739 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19560569 spots for ERR3975748/ERR3975748.sra Written 19560569 spots for ERR3975748/ERR3975748.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169519 ("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: 00:39:31 19560569 reads; of these: 19560569 (100.00%) were paired; of these: 7534650 (38.52%) aligned concordantly 0 times 4454339 (22.77%) aligned concordantly exactly 1 time 7571580 (38.71%) aligned concordantly >1 times ---- 7534650 pairs aligned concordantly 0 times; of these: 1407201 (18.68%) aligned discordantly 1 time ---- 6127449 pairs aligned 0 times concordantly or discordantly; of these: 12254898 mates make up the pairs; of these: 7881329 (64.31%) aligned 0 times 314787 (2.57%) aligned exactly 1 time 4058782 (33.12%) aligned >1 times 79.85% overall alignment rate Time searching: 00:39:31 Overall time: 00:39:31 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] 5818802 / 13331506 = 0.4365 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 18:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.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 18:16:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:16:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:16:53: 1000000 INFO @ Fri, 10 Dec 2021 18:17:00: 2000000 INFO @ Fri, 10 Dec 2021 18:17:07: 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 18:17:15: 4000000 INFO @ Fri, 10 Dec 2021 18:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.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 18:17:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:17:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:17:23: 5000000 INFO @ Fri, 10 Dec 2021 18:17:24: 1000000 INFO @ Fri, 10 Dec 2021 18:17:32: 6000000 INFO @ Fri, 10 Dec 2021 18:17:33: 2000000 INFO @ Fri, 10 Dec 2021 18:17:41: 7000000 INFO @ Fri, 10 Dec 2021 18:17:42: 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 18:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.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 18:17:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:17:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:17:50: 8000000 INFO @ Fri, 10 Dec 2021 18:17:51: 4000000 INFO @ Fri, 10 Dec 2021 18:17:57: 1000000 INFO @ Fri, 10 Dec 2021 18:18:00: 9000000 INFO @ Fri, 10 Dec 2021 18:18:01: 5000000 INFO @ Fri, 10 Dec 2021 18:18:08: 2000000 INFO @ Fri, 10 Dec 2021 18:18:10: 10000000 INFO @ Fri, 10 Dec 2021 18:18:11: 6000000 INFO @ Fri, 10 Dec 2021 18:18:19: 3000000 INFO @ Fri, 10 Dec 2021 18:18:19: 11000000 INFO @ Fri, 10 Dec 2021 18:18:21: 7000000 INFO @ Fri, 10 Dec 2021 18:18:29: 12000000 INFO @ Fri, 10 Dec 2021 18:18:31: 4000000 INFO @ Fri, 10 Dec 2021 18:18:31: 8000000 INFO @ Fri, 10 Dec 2021 18:18:38: 13000000 INFO @ Fri, 10 Dec 2021 18:18:41: 9000000 INFO @ Fri, 10 Dec 2021 18:18:42: 5000000 INFO @ Fri, 10 Dec 2021 18:18:48: 14000000 INFO @ Fri, 10 Dec 2021 18:18:51: 10000000 INFO @ Fri, 10 Dec 2021 18:18:53: 6000000 INFO @ Fri, 10 Dec 2021 18:18:57: 15000000 INFO @ Fri, 10 Dec 2021 18:19:00: 11000000 INFO @ Fri, 10 Dec 2021 18:19:05: 7000000 INFO @ Fri, 10 Dec 2021 18:19:07: 16000000 INFO @ Fri, 10 Dec 2021 18:19:10: 12000000 INFO @ Fri, 10 Dec 2021 18:19:16: 8000000 INFO @ Fri, 10 Dec 2021 18:19:17: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:19:19: 13000000 INFO @ Fri, 10 Dec 2021 18:19:26: 18000000 INFO @ Fri, 10 Dec 2021 18:19:27: 9000000 INFO @ Fri, 10 Dec 2021 18:19:29: 14000000 INFO @ Fri, 10 Dec 2021 18:19:36: 19000000 INFO @ Fri, 10 Dec 2021 18:19:38: 10000000 INFO @ Fri, 10 Dec 2021 18:19:38: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:19:42: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:19:42: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:19:42: #1 total tags in treatment: 6321823 INFO @ Fri, 10 Dec 2021 18:19:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:19:42: #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 18:19:42: #1 tags after filtering in treatment: 4545283 INFO @ Fri, 10 Dec 2021 18:19:42: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 18:19:42: #1 finished! INFO @ Fri, 10 Dec 2021 18:19:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:19:43: #2 number of paired peaks: 3157 INFO @ Fri, 10 Dec 2021 18:19:43: start model_add_line... INFO @ Fri, 10 Dec 2021 18:19:43: start X-correlation... INFO @ Fri, 10 Dec 2021 18:19:43: end of X-cor INFO @ Fri, 10 Dec 2021 18:19:43: #2 finished! INFO @ Fri, 10 Dec 2021 18:19:43: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 18:19:43: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 18:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.05_model.r WARNING @ Fri, 10 Dec 2021 18:19:43: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:19:43: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 18:19:43: #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 18:19:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:19:48: 16000000 INFO @ Fri, 10 Dec 2021 18:19:49: 11000000 INFO @ Fri, 10 Dec 2021 18:19:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:19:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.05_summits.bed INFO @ Fri, 10 Dec 2021 18:19:58: Done! INFO @ Fri, 10 Dec 2021 18:19:58: 17000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8258 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:20:00: 12000000 INFO @ Fri, 10 Dec 2021 18:20:08: 18000000 INFO @ Fri, 10 Dec 2021 18:20:10: 13000000 INFO @ Fri, 10 Dec 2021 18:20:17: 19000000 INFO @ Fri, 10 Dec 2021 18:20:21: 14000000 INFO @ Fri, 10 Dec 2021 18:20:23: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:20:23: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:20:23: #1 total tags in treatment: 6321823 INFO @ Fri, 10 Dec 2021 18:20:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:20:23: #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 18:20:23: #1 tags after filtering in treatment: 4545283 INFO @ Fri, 10 Dec 2021 18:20:23: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 18:20:23: #1 finished! INFO @ Fri, 10 Dec 2021 18:20:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:20:24: #2 number of paired peaks: 3157 INFO @ Fri, 10 Dec 2021 18:20:24: start model_add_line... INFO @ Fri, 10 Dec 2021 18:20:24: start X-correlation... INFO @ Fri, 10 Dec 2021 18:20:24: end of X-cor INFO @ Fri, 10 Dec 2021 18:20:24: #2 finished! INFO @ Fri, 10 Dec 2021 18:20:24: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 18:20:24: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 18:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.10_model.r WARNING @ Fri, 10 Dec 2021 18:20:24: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:20:24: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 18:20:24: #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 18:20:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:20:31: 15000000 INFO @ Fri, 10 Dec 2021 18:20:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:20:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:20:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:20:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.10_summits.bed INFO @ Fri, 10 Dec 2021 18:20:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4592 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:20:40: 16000000 INFO @ Fri, 10 Dec 2021 18:20:50: 17000000 INFO @ Fri, 10 Dec 2021 18:21:00: 18000000 INFO @ Fri, 10 Dec 2021 18:21:10: 19000000 INFO @ Fri, 10 Dec 2021 18:21:15: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:21:15: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:21:15: #1 total tags in treatment: 6321823 INFO @ Fri, 10 Dec 2021 18:21:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:21:15: #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 18:21:16: #1 tags after filtering in treatment: 4545283 INFO @ Fri, 10 Dec 2021 18:21:16: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 18:21:16: #1 finished! INFO @ Fri, 10 Dec 2021 18:21:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:21:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:21:16: #2 number of paired peaks: 3157 INFO @ Fri, 10 Dec 2021 18:21:16: start model_add_line... INFO @ Fri, 10 Dec 2021 18:21:16: start X-correlation... INFO @ Fri, 10 Dec 2021 18:21:16: end of X-cor INFO @ Fri, 10 Dec 2021 18:21:16: #2 finished! INFO @ Fri, 10 Dec 2021 18:21:16: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 18:21:16: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 18:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.20_model.r WARNING @ Fri, 10 Dec 2021 18:21:16: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:21:16: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 18:21:16: #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 18:21:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:21:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978739/ERX3978739.20_summits.bed INFO @ Fri, 10 Dec 2021 18:21:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1581 records, 4 fields): 3 millis CompletedMACS2peakCalling