Job ID = 14168540 SRX = ERX3978756 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14990532 spots for ERR3975769/ERR3975769.sra Written 14990532 spots for ERR3975769/ERR3975769.sra Read 19214205 spots for ERR3975811/ERR3975811.sra Written 19214205 spots for ERR3975811/ERR3975811.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169811 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:52:36 34204737 reads; of these: 34204737 (100.00%) were paired; of these: 12140886 (35.49%) aligned concordantly 0 times 3422452 (10.01%) aligned concordantly exactly 1 time 18641399 (54.50%) aligned concordantly >1 times ---- 12140886 pairs aligned concordantly 0 times; of these: 1155006 (9.51%) aligned discordantly 1 time ---- 10985880 pairs aligned 0 times concordantly or discordantly; of these: 21971760 mates make up the pairs; of these: 10457293 (47.59%) aligned 0 times 389537 (1.77%) aligned exactly 1 time 11124930 (50.63%) aligned >1 times 84.71% overall alignment rate Time searching: 00:52:37 Overall time: 00:52:37 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 40 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] 16438988 / 23005031 = 0.7146 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 20:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.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 20:09:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:09:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:09:53: 1000000 INFO @ Fri, 10 Dec 2021 20:10:00: 2000000 INFO @ Fri, 10 Dec 2021 20:10:08: 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 @ Fri, 10 Dec 2021 20:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.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 20:10:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:10:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:10:17: 4000000 INFO @ Fri, 10 Dec 2021 20:10:24: 1000000 INFO @ Fri, 10 Dec 2021 20:10:26: 5000000 INFO @ Fri, 10 Dec 2021 20:10:34: 2000000 INFO @ Fri, 10 Dec 2021 20:10:36: 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 @ Fri, 10 Dec 2021 20:10:43: 3000000 INFO @ Fri, 10 Dec 2021 20:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.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 20:10:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:10:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:10:46: 7000000 INFO @ Fri, 10 Dec 2021 20:10:52: 4000000 INFO @ Fri, 10 Dec 2021 20:10:54: 1000000 INFO @ Fri, 10 Dec 2021 20:10:55: 8000000 INFO @ Fri, 10 Dec 2021 20:11:00: 5000000 INFO @ Fri, 10 Dec 2021 20:11:04: 2000000 INFO @ Fri, 10 Dec 2021 20:11:05: 9000000 INFO @ Fri, 10 Dec 2021 20:11:09: 6000000 INFO @ Fri, 10 Dec 2021 20:11:13: 3000000 INFO @ Fri, 10 Dec 2021 20:11:14: 10000000 INFO @ Fri, 10 Dec 2021 20:11:18: 7000000 INFO @ Fri, 10 Dec 2021 20:11:22: 4000000 INFO @ Fri, 10 Dec 2021 20:11:24: 11000000 INFO @ Fri, 10 Dec 2021 20:11:27: 8000000 INFO @ Fri, 10 Dec 2021 20:11:31: 5000000 INFO @ Fri, 10 Dec 2021 20:11:33: 12000000 INFO @ Fri, 10 Dec 2021 20:11:35: 9000000 INFO @ Fri, 10 Dec 2021 20:11:40: 6000000 INFO @ Fri, 10 Dec 2021 20:11:42: 13000000 INFO @ Fri, 10 Dec 2021 20:11:43: 10000000 INFO @ Fri, 10 Dec 2021 20:11:49: 7000000 INFO @ Fri, 10 Dec 2021 20:11:51: 14000000 INFO @ Fri, 10 Dec 2021 20:11:51: 11000000 INFO @ Fri, 10 Dec 2021 20:11:58: 8000000 INFO @ Fri, 10 Dec 2021 20:11:59: 12000000 INFO @ Fri, 10 Dec 2021 20:12:00: 15000000 INFO @ Fri, 10 Dec 2021 20:12:06: 9000000 INFO @ Fri, 10 Dec 2021 20:12:07: 13000000 INFO @ Fri, 10 Dec 2021 20:12:09: 16000000 INFO @ Fri, 10 Dec 2021 20:12:14: 10000000 INFO @ Fri, 10 Dec 2021 20:12:15: 14000000 INFO @ Fri, 10 Dec 2021 20:12:18: 17000000 INFO @ Fri, 10 Dec 2021 20:12:22: 11000000 INFO @ Fri, 10 Dec 2021 20:12:24: 15000000 INFO @ Fri, 10 Dec 2021 20:12:28: 18000000 INFO @ Fri, 10 Dec 2021 20:12:30: 12000000 INFO @ Fri, 10 Dec 2021 20:12:32: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:12:37: 19000000 INFO @ Fri, 10 Dec 2021 20:12:38: 13000000 INFO @ Fri, 10 Dec 2021 20:12:40: 17000000 INFO @ Fri, 10 Dec 2021 20:12:46: 20000000 INFO @ Fri, 10 Dec 2021 20:12:47: 14000000 INFO @ Fri, 10 Dec 2021 20:12:48: 18000000 INFO @ Fri, 10 Dec 2021 20:12:55: 21000000 INFO @ Fri, 10 Dec 2021 20:12:55: 15000000 INFO @ Fri, 10 Dec 2021 20:12:57: 19000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:13:03: 16000000 INFO @ Fri, 10 Dec 2021 20:13:04: 22000000 INFO @ Fri, 10 Dec 2021 20:13:05: 20000000 INFO @ Fri, 10 Dec 2021 20:13:11: 17000000 INFO @ Fri, 10 Dec 2021 20:13:13: 21000000 INFO @ Fri, 10 Dec 2021 20:13:13: 23000000 INFO @ Fri, 10 Dec 2021 20:13:20: 18000000 INFO @ Fri, 10 Dec 2021 20:13:21: 22000000 INFO @ Fri, 10 Dec 2021 20:13:23: 24000000 INFO @ Fri, 10 Dec 2021 20:13:28: 19000000 INFO @ Fri, 10 Dec 2021 20:13:30: 23000000 INFO @ Fri, 10 Dec 2021 20:13:32: 25000000 INFO @ Fri, 10 Dec 2021 20:13:33: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:13:33: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:13:33: #1 total tags in treatment: 5752690 INFO @ Fri, 10 Dec 2021 20:13:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:13:33: #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 20:13:33: #1 tags after filtering in treatment: 3549879 INFO @ Fri, 10 Dec 2021 20:13:33: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 10 Dec 2021 20:13:33: #1 finished! INFO @ Fri, 10 Dec 2021 20:13:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:13:34: #2 number of paired peaks: 4294 INFO @ Fri, 10 Dec 2021 20:13:34: start model_add_line... INFO @ Fri, 10 Dec 2021 20:13:34: start X-correlation... INFO @ Fri, 10 Dec 2021 20:13:34: end of X-cor INFO @ Fri, 10 Dec 2021 20:13:34: #2 finished! INFO @ Fri, 10 Dec 2021 20:13:34: #2 predicted fragment length is 219 bps INFO @ Fri, 10 Dec 2021 20:13:34: #2 alternative fragment length(s) may be 219 bps INFO @ Fri, 10 Dec 2021 20:13:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.05_model.r WARNING @ Fri, 10 Dec 2021 20:13:34: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:13:34: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Fri, 10 Dec 2021 20:13:34: #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 20:13:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:13:35: 20000000 INFO @ Fri, 10 Dec 2021 20:13:38: 24000000 INFO @ Fri, 10 Dec 2021 20:13:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:13:43: 21000000 INFO @ Fri, 10 Dec 2021 20:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.05_summits.bed INFO @ Fri, 10 Dec 2021 20:13:46: Done! INFO @ Fri, 10 Dec 2021 20:13:46: 25000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7512 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:13:47: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:13:47: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:13:47: #1 total tags in treatment: 5752690 INFO @ Fri, 10 Dec 2021 20:13:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:13:47: #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 20:13:47: #1 tags after filtering in treatment: 3549879 INFO @ Fri, 10 Dec 2021 20:13:47: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 10 Dec 2021 20:13:47: #1 finished! INFO @ Fri, 10 Dec 2021 20:13:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:13:48: #2 number of paired peaks: 4294 INFO @ Fri, 10 Dec 2021 20:13:48: start model_add_line... INFO @ Fri, 10 Dec 2021 20:13:48: start X-correlation... INFO @ Fri, 10 Dec 2021 20:13:48: end of X-cor INFO @ Fri, 10 Dec 2021 20:13:48: #2 finished! INFO @ Fri, 10 Dec 2021 20:13:48: #2 predicted fragment length is 219 bps INFO @ Fri, 10 Dec 2021 20:13:48: #2 alternative fragment length(s) may be 219 bps INFO @ Fri, 10 Dec 2021 20:13:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.10_model.r WARNING @ Fri, 10 Dec 2021 20:13:48: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:13:48: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Fri, 10 Dec 2021 20:13:48: #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 20:13:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:13:50: 22000000 INFO @ Fri, 10 Dec 2021 20:13:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:13:58: 23000000 INFO @ Fri, 10 Dec 2021 20:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.10_summits.bed INFO @ Fri, 10 Dec 2021 20:14:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4167 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:14:05: 24000000 INFO @ Fri, 10 Dec 2021 20:14:12: 25000000 INFO @ Fri, 10 Dec 2021 20:14:13: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:14:13: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:14:13: #1 total tags in treatment: 5752690 INFO @ Fri, 10 Dec 2021 20:14:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:14:13: #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 20:14:13: #1 tags after filtering in treatment: 3549879 INFO @ Fri, 10 Dec 2021 20:14:13: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 10 Dec 2021 20:14:13: #1 finished! INFO @ Fri, 10 Dec 2021 20:14:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:14:13: #2 number of paired peaks: 4294 INFO @ Fri, 10 Dec 2021 20:14:13: start model_add_line... INFO @ Fri, 10 Dec 2021 20:14:13: start X-correlation... INFO @ Fri, 10 Dec 2021 20:14:13: end of X-cor INFO @ Fri, 10 Dec 2021 20:14:13: #2 finished! INFO @ Fri, 10 Dec 2021 20:14:13: #2 predicted fragment length is 219 bps INFO @ Fri, 10 Dec 2021 20:14:13: #2 alternative fragment length(s) may be 219 bps INFO @ Fri, 10 Dec 2021 20:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.20_model.r WARNING @ Fri, 10 Dec 2021 20:14:13: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:14:13: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Fri, 10 Dec 2021 20:14:13: #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 20:14:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:14:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978756/ERX3978756.20_summits.bed INFO @ Fri, 10 Dec 2021 20:14:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1418 records, 4 fields): 3 millis CompletedMACS2peakCalling