Job ID = 14167195 SRX = SRX8913800 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22850648 spots for SRR12417799/SRR12417799.sra Written 22850648 spots for SRR12417799/SRR12417799.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168885 ("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: 04:30:33 22850648 reads; of these: 22850648 (100.00%) were paired; of these: 7472742 (32.70%) aligned concordantly 0 times 3703090 (16.21%) aligned concordantly exactly 1 time 11674816 (51.09%) aligned concordantly >1 times ---- 7472742 pairs aligned concordantly 0 times; of these: 1142898 (15.29%) aligned discordantly 1 time ---- 6329844 pairs aligned 0 times concordantly or discordantly; of these: 12659688 mates make up the pairs; of these: 8312294 (65.66%) aligned 0 times 420028 (3.32%) aligned exactly 1 time 3927366 (31.02%) aligned >1 times 81.81% overall alignment rate Time searching: 04:30:33 Overall time: 04:30:33 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 28 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] 4472703 / 16238239 = 0.2754 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 15:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.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 15:44:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:44:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:45:04: 1000000 INFO @ Fri, 10 Dec 2021 15:45:10: 2000000 INFO @ Fri, 10 Dec 2021 15:45:17: 3000000 INFO @ Fri, 10 Dec 2021 15:45:23: 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 15:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.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 15:45:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:45:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:45:30: 5000000 INFO @ Fri, 10 Dec 2021 15:45:34: 1000000 INFO @ Fri, 10 Dec 2021 15:45:36: 6000000 INFO @ Fri, 10 Dec 2021 15:45:41: 2000000 INFO @ Fri, 10 Dec 2021 15:45:43: 7000000 INFO @ Fri, 10 Dec 2021 15:45:48: 3000000 INFO @ Fri, 10 Dec 2021 15:45:49: 8000000 INFO @ Fri, 10 Dec 2021 15:45:54: 4000000 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 15:45:56: 9000000 INFO @ Fri, 10 Dec 2021 15:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.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 15:45:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:45:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:46:01: 5000000 INFO @ Fri, 10 Dec 2021 15:46:03: 10000000 INFO @ Fri, 10 Dec 2021 15:46:04: 1000000 INFO @ Fri, 10 Dec 2021 15:46:08: 6000000 INFO @ Fri, 10 Dec 2021 15:46:10: 11000000 INFO @ Fri, 10 Dec 2021 15:46:11: 2000000 INFO @ Fri, 10 Dec 2021 15:46:15: 7000000 INFO @ Fri, 10 Dec 2021 15:46:17: 12000000 INFO @ Fri, 10 Dec 2021 15:46:18: 3000000 INFO @ Fri, 10 Dec 2021 15:46:21: 8000000 INFO @ Fri, 10 Dec 2021 15:46:24: 13000000 INFO @ Fri, 10 Dec 2021 15:46:24: 4000000 INFO @ Fri, 10 Dec 2021 15:46:28: 9000000 INFO @ Fri, 10 Dec 2021 15:46:30: 14000000 INFO @ Fri, 10 Dec 2021 15:46:31: 5000000 INFO @ Fri, 10 Dec 2021 15:46:35: 10000000 INFO @ Fri, 10 Dec 2021 15:46:37: 15000000 INFO @ Fri, 10 Dec 2021 15:46:38: 6000000 INFO @ Fri, 10 Dec 2021 15:46:42: 11000000 INFO @ Fri, 10 Dec 2021 15:46:44: 16000000 INFO @ Fri, 10 Dec 2021 15:46:44: 7000000 INFO @ Fri, 10 Dec 2021 15:46:49: 12000000 INFO @ Fri, 10 Dec 2021 15:46:51: 17000000 INFO @ Fri, 10 Dec 2021 15:46:51: 8000000 INFO @ Fri, 10 Dec 2021 15:46:56: 13000000 INFO @ Fri, 10 Dec 2021 15:46:57: 9000000 INFO @ Fri, 10 Dec 2021 15:46:57: 18000000 INFO @ Fri, 10 Dec 2021 15:47:02: 14000000 INFO @ Fri, 10 Dec 2021 15:47:04: 10000000 INFO @ Fri, 10 Dec 2021 15:47:04: 19000000 INFO @ Fri, 10 Dec 2021 15:47:09: 15000000 INFO @ Fri, 10 Dec 2021 15:47:11: 11000000 INFO @ Fri, 10 Dec 2021 15:47:11: 20000000 INFO @ Fri, 10 Dec 2021 15:47:16: 16000000 INFO @ Fri, 10 Dec 2021 15:47:17: 12000000 INFO @ Fri, 10 Dec 2021 15:47:18: 21000000 INFO @ Fri, 10 Dec 2021 15:47:23: 17000000 INFO @ Fri, 10 Dec 2021 15:47:24: 13000000 INFO @ Fri, 10 Dec 2021 15:47:25: 22000000 INFO @ Fri, 10 Dec 2021 15:47:29: 18000000 INFO @ Fri, 10 Dec 2021 15:47:31: 14000000 INFO @ Fri, 10 Dec 2021 15:47:32: 23000000 INFO @ Fri, 10 Dec 2021 15:47:36: 19000000 INFO @ Fri, 10 Dec 2021 15:47:37: 15000000 INFO @ Fri, 10 Dec 2021 15:47:39: 24000000 INFO @ Fri, 10 Dec 2021 15:47:43: 20000000 INFO @ Fri, 10 Dec 2021 15:47:44: 16000000 INFO @ Fri, 10 Dec 2021 15:47:46: 25000000 INFO @ Fri, 10 Dec 2021 15:47:50: 21000000 INFO @ Fri, 10 Dec 2021 15:47:51: 17000000 INFO @ Fri, 10 Dec 2021 15:47:53: 26000000 INFO @ Fri, 10 Dec 2021 15:47:57: 22000000 INFO @ Fri, 10 Dec 2021 15:47:57: 18000000 INFO @ Fri, 10 Dec 2021 15:48:00: 27000000 INFO @ Fri, 10 Dec 2021 15:48:04: 19000000 INFO @ Fri, 10 Dec 2021 15:48:04: 23000000 INFO @ Fri, 10 Dec 2021 15:48:07: 28000000 INFO @ Fri, 10 Dec 2021 15:48:10: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 15:48:10: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 15:48:10: #1 total tags in treatment: 10996736 INFO @ Fri, 10 Dec 2021 15:48:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:48:10: #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 15:48:10: #1 tags after filtering in treatment: 7594462 INFO @ Fri, 10 Dec 2021 15:48:10: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 15:48:10: #1 finished! INFO @ Fri, 10 Dec 2021 15:48:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:48:10: 20000000 INFO @ Fri, 10 Dec 2021 15:48:11: #2 number of paired peaks: 2913 INFO @ Fri, 10 Dec 2021 15:48:11: start model_add_line... INFO @ Fri, 10 Dec 2021 15:48:11: 24000000 INFO @ Fri, 10 Dec 2021 15:48:11: start X-correlation... INFO @ Fri, 10 Dec 2021 15:48:11: end of X-cor INFO @ Fri, 10 Dec 2021 15:48:11: #2 finished! INFO @ Fri, 10 Dec 2021 15:48:11: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 15:48:11: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 15:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.05_model.r WARNING @ Fri, 10 Dec 2021 15:48:11: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:48:11: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 15:48:11: #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 15:48:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:48:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:48:17: 21000000 INFO @ Fri, 10 Dec 2021 15:48:18: 25000000 INFO @ Fri, 10 Dec 2021 15:48:24: 22000000 INFO @ Fri, 10 Dec 2021 15:48:25: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:48:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:48:31: 23000000 INFO @ Fri, 10 Dec 2021 15:48:32: 27000000 INFO @ Fri, 10 Dec 2021 15:48:38: 24000000 INFO @ Fri, 10 Dec 2021 15:48:38: 28000000 INFO @ Fri, 10 Dec 2021 15:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.05_summits.bed INFO @ Fri, 10 Dec 2021 15:48:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10400 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:48:41: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 15:48:41: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 15:48:41: #1 total tags in treatment: 10996736 INFO @ Fri, 10 Dec 2021 15:48:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:48:41: #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 15:48:41: #1 tags after filtering in treatment: 7594462 INFO @ Fri, 10 Dec 2021 15:48:41: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 15:48:41: #1 finished! INFO @ Fri, 10 Dec 2021 15:48:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:48:42: #2 number of paired peaks: 2913 INFO @ Fri, 10 Dec 2021 15:48:42: start model_add_line... INFO @ Fri, 10 Dec 2021 15:48:42: start X-correlation... INFO @ Fri, 10 Dec 2021 15:48:42: end of X-cor INFO @ Fri, 10 Dec 2021 15:48:42: #2 finished! INFO @ Fri, 10 Dec 2021 15:48:42: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 15:48:42: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 15:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.10_model.r WARNING @ Fri, 10 Dec 2021 15:48:42: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:48:42: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 15:48:42: #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 15:48:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:48:44: 25000000 INFO @ Fri, 10 Dec 2021 15:48:51: 26000000 INFO @ Fri, 10 Dec 2021 15:48:58: 27000000 INFO @ Fri, 10 Dec 2021 15:49:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:49:04: 28000000 INFO @ Fri, 10 Dec 2021 15:49:07: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 15:49:07: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 15:49:07: #1 total tags in treatment: 10996736 INFO @ Fri, 10 Dec 2021 15:49:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:49:07: #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 15:49:07: #1 tags after filtering in treatment: 7594462 INFO @ Fri, 10 Dec 2021 15:49:07: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 15:49:07: #1 finished! INFO @ Fri, 10 Dec 2021 15:49:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:49:08: #2 number of paired peaks: 2913 INFO @ Fri, 10 Dec 2021 15:49:08: start model_add_line... INFO @ Fri, 10 Dec 2021 15:49:08: start X-correlation... INFO @ Fri, 10 Dec 2021 15:49:08: end of X-cor INFO @ Fri, 10 Dec 2021 15:49:08: #2 finished! INFO @ Fri, 10 Dec 2021 15:49:08: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 15:49:08: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 15:49:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.20_model.r WARNING @ Fri, 10 Dec 2021 15:49:08: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:49:08: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 15:49:08: #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 15:49:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:49:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.10_summits.bed INFO @ Fri, 10 Dec 2021 15:49:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6346 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:49:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:49:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:49:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:49:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8913800/SRX8913800.20_summits.bed INFO @ Fri, 10 Dec 2021 15:49:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3412 records, 4 fields): 7 millis CompletedMACS2peakCalling