Job ID = 14170886 SRX = SRX11704573 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T23:56:15 prefetch.2.10.7: 1) Downloading 'SRR15402357'... 2021-12-10T23:56:15 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T23:58:56 prefetch.2.10.7: HTTPS download succeed 2021-12-10T23:58:56 prefetch.2.10.7: 1) 'SRR15402357' was downloaded successfully 2021-12-10T23:58:56 prefetch.2.10.7: 'SRR15402357' has 0 unresolved dependencies Read 87147132 spots for SRR15402357/SRR15402357.sra Written 87147132 spots for SRR15402357/SRR15402357.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171577 ("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: 00:38:51 87147132 reads; of these: 87147132 (100.00%) were paired; of these: 80579770 (92.46%) aligned concordantly 0 times 6056498 (6.95%) aligned concordantly exactly 1 time 510864 (0.59%) aligned concordantly >1 times ---- 80579770 pairs aligned concordantly 0 times; of these: 1280604 (1.59%) aligned discordantly 1 time ---- 79299166 pairs aligned 0 times concordantly or discordantly; of these: 158598332 mates make up the pairs; of these: 148912016 (93.89%) aligned 0 times 431040 (0.27%) aligned exactly 1 time 9255276 (5.84%) aligned >1 times 14.56% overall alignment rate Time searching: 00:38:52 Overall time: 00:38:52 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 12 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] 2023461 / 7718857 = 0.2621 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 09:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.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 09:49:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:49:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:49:26: 1000000 INFO @ Sat, 11 Dec 2021 09:49:31: 2000000 INFO @ Sat, 11 Dec 2021 09:49:36: 3000000 INFO @ Sat, 11 Dec 2021 09:49:41: 4000000 INFO @ Sat, 11 Dec 2021 09:49:47: 5000000 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 09:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.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 09:49:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:49:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:49:52: 6000000 INFO @ Sat, 11 Dec 2021 09:49:56: 1000000 INFO @ Sat, 11 Dec 2021 09:49:58: 7000000 INFO @ Sat, 11 Dec 2021 09:50:01: 2000000 INFO @ Sat, 11 Dec 2021 09:50:03: 8000000 INFO @ Sat, 11 Dec 2021 09:50:06: 3000000 INFO @ Sat, 11 Dec 2021 09:50:09: 9000000 INFO @ Sat, 11 Dec 2021 09:50:11: 4000000 INFO @ Sat, 11 Dec 2021 09:50:14: 10000000 INFO @ Sat, 11 Dec 2021 09:50:16: 5000000 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 09:50:19: 11000000 INFO @ Sat, 11 Dec 2021 09:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.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 09:50:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:50:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:50:21: 6000000 INFO @ Sat, 11 Dec 2021 09:50:23: 12000000 INFO @ Sat, 11 Dec 2021 09:50:26: 1000000 INFO @ Sat, 11 Dec 2021 09:50:26: 7000000 INFO @ Sat, 11 Dec 2021 09:50:29: 13000000 INFO @ Sat, 11 Dec 2021 09:50:31: 2000000 INFO @ Sat, 11 Dec 2021 09:50:31: 8000000 INFO @ Sat, 11 Dec 2021 09:50:34: 14000000 INFO @ Sat, 11 Dec 2021 09:50:36: 3000000 INFO @ Sat, 11 Dec 2021 09:50:36: 9000000 INFO @ Sat, 11 Dec 2021 09:50:39: 15000000 INFO @ Sat, 11 Dec 2021 09:50:41: 10000000 INFO @ Sat, 11 Dec 2021 09:50:41: 4000000 INFO @ Sat, 11 Dec 2021 09:50:43: 16000000 INFO @ Sat, 11 Dec 2021 09:50:45: 11000000 INFO @ Sat, 11 Dec 2021 09:50:46: 5000000 INFO @ Sat, 11 Dec 2021 09:50:48: 17000000 INFO @ Sat, 11 Dec 2021 09:50:50: 12000000 INFO @ Sat, 11 Dec 2021 09:50:51: 6000000 INFO @ Sat, 11 Dec 2021 09:50:53: 18000000 INFO @ Sat, 11 Dec 2021 09:50:54: 13000000 INFO @ Sat, 11 Dec 2021 09:50:56: 7000000 INFO @ Sat, 11 Dec 2021 09:50:58: 19000000 INFO @ Sat, 11 Dec 2021 09:50:59: 14000000 INFO @ Sat, 11 Dec 2021 09:51:01: 8000000 INFO @ Sat, 11 Dec 2021 09:51:03: 15000000 INFO @ Sat, 11 Dec 2021 09:51:03: 20000000 INFO @ Sat, 11 Dec 2021 09:51:06: 9000000 INFO @ Sat, 11 Dec 2021 09:51:08: 16000000 INFO @ Sat, 11 Dec 2021 09:51:09: 21000000 INFO @ Sat, 11 Dec 2021 09:51:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:51:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:51:11: #1 total tags in treatment: 4951286 INFO @ Sat, 11 Dec 2021 09:51:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:51:11: #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 09:51:11: #1 tags after filtering in treatment: 3204177 INFO @ Sat, 11 Dec 2021 09:51:11: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 09:51:11: #1 finished! INFO @ Sat, 11 Dec 2021 09:51:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:51:11: 10000000 INFO @ Sat, 11 Dec 2021 09:51:11: #2 number of paired peaks: 8423 INFO @ Sat, 11 Dec 2021 09:51:11: start model_add_line... INFO @ Sat, 11 Dec 2021 09:51:11: start X-correlation... INFO @ Sat, 11 Dec 2021 09:51:11: end of X-cor INFO @ Sat, 11 Dec 2021 09:51:11: #2 finished! INFO @ Sat, 11 Dec 2021 09:51:11: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 09:51:11: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 09:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.05_model.r WARNING @ Sat, 11 Dec 2021 09:51:11: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:51:11: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 09:51:11: #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 09:51:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:51:12: 17000000 INFO @ Sat, 11 Dec 2021 09:51:16: 11000000 INFO @ Sat, 11 Dec 2021 09:51:16: 18000000 INFO @ Sat, 11 Dec 2021 09:51:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:51:20: 12000000 INFO @ Sat, 11 Dec 2021 09:51:20: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.05_summits.bed INFO @ Sat, 11 Dec 2021 09:51:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13551 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:51:25: 13000000 INFO @ Sat, 11 Dec 2021 09:51:25: 20000000 INFO @ Sat, 11 Dec 2021 09:51:29: 14000000 INFO @ Sat, 11 Dec 2021 09:51:30: 21000000 INFO @ Sat, 11 Dec 2021 09:51:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:51:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:51:32: #1 total tags in treatment: 4951286 INFO @ Sat, 11 Dec 2021 09:51:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:51:32: #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 09:51:32: #1 tags after filtering in treatment: 3204177 INFO @ Sat, 11 Dec 2021 09:51:32: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 09:51:32: #1 finished! INFO @ Sat, 11 Dec 2021 09:51:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:51:33: #2 number of paired peaks: 8423 INFO @ Sat, 11 Dec 2021 09:51:33: start model_add_line... INFO @ Sat, 11 Dec 2021 09:51:33: start X-correlation... INFO @ Sat, 11 Dec 2021 09:51:33: end of X-cor INFO @ Sat, 11 Dec 2021 09:51:33: #2 finished! INFO @ Sat, 11 Dec 2021 09:51:33: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 09:51:33: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 09:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.10_model.r WARNING @ Sat, 11 Dec 2021 09:51:33: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:51:33: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 09:51:33: #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 09:51:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:51:33: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:51:37: 16000000 INFO @ Sat, 11 Dec 2021 09:51:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:51:41: 17000000 INFO @ Sat, 11 Dec 2021 09:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.10_summits.bed INFO @ Sat, 11 Dec 2021 09:51:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9314 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:51:45: 18000000 INFO @ Sat, 11 Dec 2021 09:51:49: 19000000 INFO @ Sat, 11 Dec 2021 09:51:53: 20000000 INFO @ Sat, 11 Dec 2021 09:51:58: 21000000 INFO @ Sat, 11 Dec 2021 09:52:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:52:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:52:00: #1 total tags in treatment: 4951286 INFO @ Sat, 11 Dec 2021 09:52:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:52:00: #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 09:52:00: #1 tags after filtering in treatment: 3204177 INFO @ Sat, 11 Dec 2021 09:52:00: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 11 Dec 2021 09:52:00: #1 finished! INFO @ Sat, 11 Dec 2021 09:52:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:52:00: #2 number of paired peaks: 8423 INFO @ Sat, 11 Dec 2021 09:52:00: start model_add_line... INFO @ Sat, 11 Dec 2021 09:52:00: start X-correlation... INFO @ Sat, 11 Dec 2021 09:52:00: end of X-cor INFO @ Sat, 11 Dec 2021 09:52:00: #2 finished! INFO @ Sat, 11 Dec 2021 09:52:00: #2 predicted fragment length is 81 bps INFO @ Sat, 11 Dec 2021 09:52:00: #2 alternative fragment length(s) may be 81 bps INFO @ Sat, 11 Dec 2021 09:52:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.20_model.r WARNING @ Sat, 11 Dec 2021 09:52:00: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:52:00: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sat, 11 Dec 2021 09:52:00: #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 09:52:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:52:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:52:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704573/SRX11704573.20_summits.bed INFO @ Sat, 11 Dec 2021 09:52:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4803 records, 4 fields): 6 millis CompletedMACS2peakCalling