Job ID = 14168183 SRX = ERX3978833 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30013112 spots for ERR3975902/ERR3975902.sra Written 30013112 spots for ERR3975902/ERR3975902.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169497 ("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: 01:59:18 30013112 reads; of these: 30013112 (100.00%) were paired; of these: 10174924 (33.90%) aligned concordantly 0 times 15498722 (51.64%) aligned concordantly exactly 1 time 4339466 (14.46%) aligned concordantly >1 times ---- 10174924 pairs aligned concordantly 0 times; of these: 1104042 (10.85%) aligned discordantly 1 time ---- 9070882 pairs aligned 0 times concordantly or discordantly; of these: 18141764 mates make up the pairs; of these: 8509651 (46.91%) aligned 0 times 5537089 (30.52%) aligned exactly 1 time 4095024 (22.57%) aligned >1 times 85.82% overall alignment rate Time searching: 01:59:18 Overall time: 01:59:18 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] 17013280 / 20583063 = 0.8266 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 18:11:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.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 18:11:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:12:00: 1000000 INFO @ Fri, 10 Dec 2021 18:12:05: 2000000 INFO @ Fri, 10 Dec 2021 18:12:11: 3000000 INFO @ Fri, 10 Dec 2021 18:12:16: 4000000 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 18:12:22: 5000000 INFO @ Fri, 10 Dec 2021 18:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.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 18:12:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:12:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:12:28: 6000000 INFO @ Fri, 10 Dec 2021 18:12:30: 1000000 INFO @ Fri, 10 Dec 2021 18:12:34: 7000000 INFO @ Fri, 10 Dec 2021 18:12:40: 2000000 INFO @ Fri, 10 Dec 2021 18:12:41: 8000000 INFO @ Fri, 10 Dec 2021 18:12:48: 3000000 INFO @ Fri, 10 Dec 2021 18:12:49: 9000000 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 18:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.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 18:12:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:12:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:12:56: 10000000 INFO @ Fri, 10 Dec 2021 18:12:56: 4000000 INFO @ Fri, 10 Dec 2021 18:13:03: 5000000 INFO @ Fri, 10 Dec 2021 18:13:04: 11000000 INFO @ Fri, 10 Dec 2021 18:13:05: 1000000 INFO @ Fri, 10 Dec 2021 18:13:10: 6000000 INFO @ Fri, 10 Dec 2021 18:13:13: 12000000 INFO @ Fri, 10 Dec 2021 18:13:13: 2000000 INFO @ Fri, 10 Dec 2021 18:13:17: 7000000 INFO @ Fri, 10 Dec 2021 18:13:21: 3000000 INFO @ Fri, 10 Dec 2021 18:13:21: 13000000 INFO @ Fri, 10 Dec 2021 18:13:24: 8000000 INFO @ Fri, 10 Dec 2021 18:13:27: 4000000 INFO @ Fri, 10 Dec 2021 18:13:28: 14000000 INFO @ Fri, 10 Dec 2021 18:13:30: 9000000 INFO @ Fri, 10 Dec 2021 18:13:34: 5000000 INFO @ Fri, 10 Dec 2021 18:13:35: 15000000 INFO @ Fri, 10 Dec 2021 18:13:37: 10000000 INFO @ Fri, 10 Dec 2021 18:13:40: 6000000 INFO @ Fri, 10 Dec 2021 18:13:42: 16000000 INFO @ Fri, 10 Dec 2021 18:13:44: 11000000 INFO @ Fri, 10 Dec 2021 18:13:47: 7000000 INFO @ Fri, 10 Dec 2021 18:13:48: 17000000 INFO @ Fri, 10 Dec 2021 18:13:50: 12000000 INFO @ Fri, 10 Dec 2021 18:13:51: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:13:51: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:13:51: #1 total tags in treatment: 3539838 INFO @ Fri, 10 Dec 2021 18:13:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:51: #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 18:13:51: #1 tags after filtering in treatment: 2983447 INFO @ Fri, 10 Dec 2021 18:13:51: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 18:13:51: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:52: #2 number of paired peaks: 4087 INFO @ Fri, 10 Dec 2021 18:13:52: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:52: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:52: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:52: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:52: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 18:13:52: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 18:13:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.05_model.r WARNING @ Fri, 10 Dec 2021 18:13:52: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:13:52: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 18:13:52: #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 18:13:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:53: 8000000 INFO @ Fri, 10 Dec 2021 18:13:57: 13000000 INFO @ Fri, 10 Dec 2021 18:13:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:00: 9000000 INFO @ Fri, 10 Dec 2021 18:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.05_summits.bed INFO @ Fri, 10 Dec 2021 18:14:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8486 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:14:04: 14000000 INFO @ Fri, 10 Dec 2021 18:14:06: 10000000 INFO @ Fri, 10 Dec 2021 18:14:10: 15000000 INFO @ Fri, 10 Dec 2021 18:14:12: 11000000 INFO @ Fri, 10 Dec 2021 18:14:17: 16000000 INFO @ Fri, 10 Dec 2021 18:14:19: 12000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:14:23: 17000000 INFO @ Fri, 10 Dec 2021 18:14:26: 13000000 INFO @ Fri, 10 Dec 2021 18:14:26: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:14:26: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:14:26: #1 total tags in treatment: 3539838 INFO @ Fri, 10 Dec 2021 18:14:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:14:26: #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 18:14:26: #1 tags after filtering in treatment: 2983447 INFO @ Fri, 10 Dec 2021 18:14:26: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 18:14:26: #1 finished! INFO @ Fri, 10 Dec 2021 18:14:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:14:26: #2 number of paired peaks: 4087 INFO @ Fri, 10 Dec 2021 18:14:26: start model_add_line... INFO @ Fri, 10 Dec 2021 18:14:26: start X-correlation... INFO @ Fri, 10 Dec 2021 18:14:26: end of X-cor INFO @ Fri, 10 Dec 2021 18:14:26: #2 finished! INFO @ Fri, 10 Dec 2021 18:14:26: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 18:14:26: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 18:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.10_model.r WARNING @ Fri, 10 Dec 2021 18:14:26: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:14:26: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 18:14:26: #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 18:14:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:14:32: 14000000 INFO @ Fri, 10 Dec 2021 18:14:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.10_summits.bed INFO @ Fri, 10 Dec 2021 18:14:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4577 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:14:38: 15000000 INFO @ Fri, 10 Dec 2021 18:14:44: 16000000 INFO @ Fri, 10 Dec 2021 18:14:49: 17000000 INFO @ Fri, 10 Dec 2021 18:14:52: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:14:52: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:14:52: #1 total tags in treatment: 3539838 INFO @ Fri, 10 Dec 2021 18:14:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:14:52: #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 18:14:52: #1 tags after filtering in treatment: 2983447 INFO @ Fri, 10 Dec 2021 18:14:52: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 10 Dec 2021 18:14:52: #1 finished! INFO @ Fri, 10 Dec 2021 18:14:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:14:53: #2 number of paired peaks: 4087 INFO @ Fri, 10 Dec 2021 18:14:53: start model_add_line... INFO @ Fri, 10 Dec 2021 18:14:53: start X-correlation... INFO @ Fri, 10 Dec 2021 18:14:53: end of X-cor INFO @ Fri, 10 Dec 2021 18:14:53: #2 finished! INFO @ Fri, 10 Dec 2021 18:14:53: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 18:14:53: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 18:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.20_model.r WARNING @ Fri, 10 Dec 2021 18:14:53: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:14:53: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 18:14:53: #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 18:14:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:15:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978833/ERX3978833.20_summits.bed INFO @ Fri, 10 Dec 2021 18:15:03: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1578 records, 4 fields): 4 millis CompletedMACS2peakCalling