Job ID = 14169018 SRX = ERX3978782 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17420561 spots for ERR3975806/ERR3975806.sra Written 17420561 spots for ERR3975806/ERR3975806.sra Read 22846285 spots for ERR3975812/ERR3975812.sra Written 22846285 spots for ERR3975812/ERR3975812.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170301 ("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: 01:00:58 40266846 reads; of these: 40266846 (100.00%) were paired; of these: 16566527 (41.14%) aligned concordantly 0 times 5105521 (12.68%) aligned concordantly exactly 1 time 18594798 (46.18%) aligned concordantly >1 times ---- 16566527 pairs aligned concordantly 0 times; of these: 1700997 (10.27%) aligned discordantly 1 time ---- 14865530 pairs aligned 0 times concordantly or discordantly; of these: 29731060 mates make up the pairs; of these: 14405006 (48.45%) aligned 0 times 584884 (1.97%) aligned exactly 1 time 14741170 (49.58%) aligned >1 times 82.11% overall alignment rate Time searching: 01:00:58 Overall time: 01:00:58 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 48 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] 16683755 / 25126104 = 0.6640 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 00:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.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 00:21:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:21:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:21:52: 1000000 INFO @ Sat, 11 Dec 2021 00:22:01: 2000000 INFO @ Sat, 11 Dec 2021 00:22:08: 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 00:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.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 00:22:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:22:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:22:17: 4000000 INFO @ Sat, 11 Dec 2021 00:22:24: 1000000 INFO @ Sat, 11 Dec 2021 00:22:28: 5000000 INFO @ Sat, 11 Dec 2021 00:22:36: 2000000 INFO @ Sat, 11 Dec 2021 00:22:37: 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 00:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.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 00:22:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:22:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:22:47: 7000000 INFO @ Sat, 11 Dec 2021 00:22:47: 3000000 INFO @ Sat, 11 Dec 2021 00:22:55: 1000000 INFO @ Sat, 11 Dec 2021 00:22:57: 8000000 INFO @ Sat, 11 Dec 2021 00:22:59: 4000000 INFO @ Sat, 11 Dec 2021 00:23:06: 2000000 INFO @ Sat, 11 Dec 2021 00:23:07: 9000000 INFO @ Sat, 11 Dec 2021 00:23:10: 5000000 INFO @ Sat, 11 Dec 2021 00:23:16: 10000000 INFO @ Sat, 11 Dec 2021 00:23:17: 3000000 INFO @ Sat, 11 Dec 2021 00:23:21: 6000000 INFO @ Sat, 11 Dec 2021 00:23:26: 11000000 INFO @ Sat, 11 Dec 2021 00:23:29: 4000000 INFO @ Sat, 11 Dec 2021 00:23:33: 7000000 INFO @ Sat, 11 Dec 2021 00:23:36: 12000000 INFO @ Sat, 11 Dec 2021 00:23:40: 5000000 INFO @ Sat, 11 Dec 2021 00:23:44: 8000000 INFO @ Sat, 11 Dec 2021 00:23:45: 13000000 INFO @ Sat, 11 Dec 2021 00:23:51: 6000000 INFO @ Sat, 11 Dec 2021 00:23:55: 14000000 INFO @ Sat, 11 Dec 2021 00:23:56: 9000000 INFO @ Sat, 11 Dec 2021 00:24:02: 7000000 INFO @ Sat, 11 Dec 2021 00:24:05: 15000000 INFO @ Sat, 11 Dec 2021 00:24:07: 10000000 INFO @ Sat, 11 Dec 2021 00:24:13: 8000000 INFO @ Sat, 11 Dec 2021 00:24:14: 16000000 INFO @ Sat, 11 Dec 2021 00:24:18: 11000000 INFO @ Sat, 11 Dec 2021 00:24:24: 17000000 INFO @ Sat, 11 Dec 2021 00:24:24: 9000000 INFO @ Sat, 11 Dec 2021 00:24:29: 12000000 INFO @ Sat, 11 Dec 2021 00:24:33: 18000000 INFO @ Sat, 11 Dec 2021 00:24:34: 10000000 INFO @ Sat, 11 Dec 2021 00:24:40: 13000000 INFO @ Sat, 11 Dec 2021 00:24:42: 19000000 INFO @ Sat, 11 Dec 2021 00:24:45: 11000000 INFO @ Sat, 11 Dec 2021 00:24:51: 20000000 INFO @ Sat, 11 Dec 2021 00:24:51: 14000000 INFO @ Sat, 11 Dec 2021 00:24:56: 12000000 INFO @ Sat, 11 Dec 2021 00:25:00: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:25:02: 15000000 INFO @ Sat, 11 Dec 2021 00:25:07: 13000000 INFO @ Sat, 11 Dec 2021 00:25:10: 22000000 INFO @ Sat, 11 Dec 2021 00:25:13: 16000000 INFO @ Sat, 11 Dec 2021 00:25:18: 14000000 INFO @ Sat, 11 Dec 2021 00:25:19: 23000000 INFO @ Sat, 11 Dec 2021 00:25:24: 17000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:25:28: 15000000 INFO @ Sat, 11 Dec 2021 00:25:28: 24000000 INFO @ Sat, 11 Dec 2021 00:25:35: 18000000 INFO @ Sat, 11 Dec 2021 00:25:38: 25000000 INFO @ Sat, 11 Dec 2021 00:25:39: 16000000 INFO @ Sat, 11 Dec 2021 00:25:46: 19000000 INFO @ Sat, 11 Dec 2021 00:25:47: 26000000 INFO @ Sat, 11 Dec 2021 00:25:49: 17000000 INFO @ Sat, 11 Dec 2021 00:25:56: 27000000 INFO @ Sat, 11 Dec 2021 00:25:57: 20000000 INFO @ Sat, 11 Dec 2021 00:26:00: 18000000 INFO @ Sat, 11 Dec 2021 00:26:05: 28000000 INFO @ Sat, 11 Dec 2021 00:26:08: 21000000 INFO @ Sat, 11 Dec 2021 00:26:10: 19000000 INFO @ Sat, 11 Dec 2021 00:26:15: 29000000 INFO @ Sat, 11 Dec 2021 00:26:19: 22000000 INFO @ Sat, 11 Dec 2021 00:26:21: 20000000 INFO @ Sat, 11 Dec 2021 00:26:24: 30000000 INFO @ Sat, 11 Dec 2021 00:26:30: 23000000 INFO @ Sat, 11 Dec 2021 00:26:32: 21000000 INFO @ Sat, 11 Dec 2021 00:26:34: 31000000 INFO @ Sat, 11 Dec 2021 00:26:41: 24000000 INFO @ Sat, 11 Dec 2021 00:26:42: 22000000 INFO @ Sat, 11 Dec 2021 00:26:44: 32000000 INFO @ Sat, 11 Dec 2021 00:26:51: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 00:26:51: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 00:26:51: #1 total tags in treatment: 7220106 INFO @ Sat, 11 Dec 2021 00:26:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:26:51: #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 00:26:51: #1 tags after filtering in treatment: 4959757 INFO @ Sat, 11 Dec 2021 00:26:51: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 11 Dec 2021 00:26:51: #1 finished! INFO @ Sat, 11 Dec 2021 00:26:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:26:52: #2 number of paired peaks: 3244 INFO @ Sat, 11 Dec 2021 00:26:52: start model_add_line... INFO @ Sat, 11 Dec 2021 00:26:52: start X-correlation... INFO @ Sat, 11 Dec 2021 00:26:52: end of X-cor INFO @ Sat, 11 Dec 2021 00:26:52: #2 finished! INFO @ Sat, 11 Dec 2021 00:26:52: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 00:26:52: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 00:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.05_model.r WARNING @ Sat, 11 Dec 2021 00:26:52: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:26:52: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 11 Dec 2021 00:26:52: #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 00:26:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:26:52: 25000000 INFO @ Sat, 11 Dec 2021 00:26:53: 23000000 INFO @ Sat, 11 Dec 2021 00:27:03: 26000000 INFO @ Sat, 11 Dec 2021 00:27:03: 24000000 INFO @ Sat, 11 Dec 2021 00:27:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.05_summits.bed INFO @ Sat, 11 Dec 2021 00:27:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8126 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:27:14: 27000000 INFO @ Sat, 11 Dec 2021 00:27:14: 25000000 INFO @ Sat, 11 Dec 2021 00:27:24: 26000000 INFO @ Sat, 11 Dec 2021 00:27:24: 28000000 INFO @ Sat, 11 Dec 2021 00:27:35: 27000000 INFO @ Sat, 11 Dec 2021 00:27:35: 29000000 INFO @ Sat, 11 Dec 2021 00:27:45: 28000000 INFO @ Sat, 11 Dec 2021 00:27:47: 30000000 INFO @ Sat, 11 Dec 2021 00:27:55: 29000000 INFO @ Sat, 11 Dec 2021 00:27:58: 31000000 INFO @ Sat, 11 Dec 2021 00:28:06: 30000000 INFO @ Sat, 11 Dec 2021 00:28:09: 32000000 INFO @ Sat, 11 Dec 2021 00:28:17: 31000000 INFO @ Sat, 11 Dec 2021 00:28:17: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 00:28:17: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 00:28:17: #1 total tags in treatment: 7220106 INFO @ Sat, 11 Dec 2021 00:28:17: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:28:17: #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 00:28:17: #1 tags after filtering in treatment: 4959757 INFO @ Sat, 11 Dec 2021 00:28:17: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 11 Dec 2021 00:28:17: #1 finished! INFO @ Sat, 11 Dec 2021 00:28:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:28:18: #2 number of paired peaks: 3244 INFO @ Sat, 11 Dec 2021 00:28:18: start model_add_line... INFO @ Sat, 11 Dec 2021 00:28:18: start X-correlation... INFO @ Sat, 11 Dec 2021 00:28:18: end of X-cor INFO @ Sat, 11 Dec 2021 00:28:18: #2 finished! INFO @ Sat, 11 Dec 2021 00:28:18: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 00:28:18: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 00:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.10_model.r WARNING @ Sat, 11 Dec 2021 00:28:18: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:28:18: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 11 Dec 2021 00:28:18: #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 00:28:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:28:27: 32000000 INFO @ Sat, 11 Dec 2021 00:28:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:28:35: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 00:28:35: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 00:28:35: #1 total tags in treatment: 7220106 INFO @ Sat, 11 Dec 2021 00:28:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:28:35: #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 00:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.10_summits.bed INFO @ Sat, 11 Dec 2021 00:28:35: Done! INFO @ Sat, 11 Dec 2021 00:28:35: #1 tags after filtering in treatment: 4959757 INFO @ Sat, 11 Dec 2021 00:28:35: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 11 Dec 2021 00:28:35: #1 finished! INFO @ Sat, 11 Dec 2021 00:28:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:28:35: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4477 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:28:35: #2 number of paired peaks: 3244 INFO @ Sat, 11 Dec 2021 00:28:35: start model_add_line... INFO @ Sat, 11 Dec 2021 00:28:35: start X-correlation... INFO @ Sat, 11 Dec 2021 00:28:35: end of X-cor INFO @ Sat, 11 Dec 2021 00:28:35: #2 finished! INFO @ Sat, 11 Dec 2021 00:28:35: #2 predicted fragment length is 209 bps INFO @ Sat, 11 Dec 2021 00:28:35: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 11 Dec 2021 00:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.20_model.r WARNING @ Sat, 11 Dec 2021 00:28:36: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:28:36: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 11 Dec 2021 00:28:36: #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 00:28:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:28:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:28:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:28:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:28:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978782/ERX3978782.20_summits.bed INFO @ Sat, 11 Dec 2021 00:28:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1536 records, 4 fields): 3 millis CompletedMACS2peakCalling