Job ID = 16439988 SRX = SRX12175825 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29774383 spots for SRR15884964/SRR15884964.sra Written 29774383 spots for SRR15884964/SRR15884964.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440972 ("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: 01:39:48 29774383 reads; of these: 29774383 (100.00%) were paired; of these: 17120716 (57.50%) aligned concordantly 0 times 10112562 (33.96%) aligned concordantly exactly 1 time 2541105 (8.53%) aligned concordantly >1 times ---- 17120716 pairs aligned concordantly 0 times; of these: 3811898 (22.26%) aligned discordantly 1 time ---- 13308818 pairs aligned 0 times concordantly or discordantly; of these: 26617636 mates make up the pairs; of these: 24039810 (90.32%) aligned 0 times 1095315 (4.11%) aligned exactly 1 time 1482511 (5.57%) aligned >1 times 59.63% overall alignment rate Time searching: 01:39:48 Overall time: 01:39:48 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] 2643794 / 16397020 = 0.1612 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.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 @ Tue, 02 Aug 2022 18:36:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:36:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:37:09: 1000000 INFO @ Tue, 02 Aug 2022 18:37:20: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:37:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.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 @ Tue, 02 Aug 2022 18:37:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:37:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:37:31: 3000000 INFO @ Tue, 02 Aug 2022 18:37:35: 1000000 INFO @ Tue, 02 Aug 2022 18:37:42: 4000000 INFO @ Tue, 02 Aug 2022 18:37:47: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:37:54: 5000000 INFO @ Tue, 02 Aug 2022 18:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.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 @ Tue, 02 Aug 2022 18:37:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:37:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:37:59: 3000000 INFO @ Tue, 02 Aug 2022 18:38:06: 6000000 INFO @ Tue, 02 Aug 2022 18:38:10: 1000000 INFO @ Tue, 02 Aug 2022 18:38:11: 4000000 INFO @ Tue, 02 Aug 2022 18:38:18: 7000000 INFO @ Tue, 02 Aug 2022 18:38:23: 5000000 INFO @ Tue, 02 Aug 2022 18:38:25: 2000000 INFO @ Tue, 02 Aug 2022 18:38:30: 8000000 INFO @ Tue, 02 Aug 2022 18:38:35: 6000000 INFO @ Tue, 02 Aug 2022 18:38:39: 3000000 INFO @ Tue, 02 Aug 2022 18:38:42: 9000000 INFO @ Tue, 02 Aug 2022 18:38:47: 7000000 INFO @ Tue, 02 Aug 2022 18:38:54: 10000000 INFO @ Tue, 02 Aug 2022 18:38:55: 4000000 INFO @ Tue, 02 Aug 2022 18:38:59: 8000000 INFO @ Tue, 02 Aug 2022 18:39:06: 11000000 INFO @ Tue, 02 Aug 2022 18:39:11: 5000000 INFO @ Tue, 02 Aug 2022 18:39:11: 9000000 INFO @ Tue, 02 Aug 2022 18:39:19: 12000000 INFO @ Tue, 02 Aug 2022 18:39:24: 10000000 INFO @ Tue, 02 Aug 2022 18:39:26: 6000000 INFO @ Tue, 02 Aug 2022 18:39:31: 13000000 INFO @ Tue, 02 Aug 2022 18:39:36: 11000000 INFO @ Tue, 02 Aug 2022 18:39:41: 7000000 INFO @ Tue, 02 Aug 2022 18:39:43: 14000000 INFO @ Tue, 02 Aug 2022 18:39:48: 12000000 INFO @ Tue, 02 Aug 2022 18:39:55: 15000000 INFO @ Tue, 02 Aug 2022 18:39:56: 8000000 INFO @ Tue, 02 Aug 2022 18:40:00: 13000000 INFO @ Tue, 02 Aug 2022 18:40:07: 16000000 INFO @ Tue, 02 Aug 2022 18:40:11: 9000000 INFO @ Tue, 02 Aug 2022 18:40:13: 14000000 INFO @ Tue, 02 Aug 2022 18:40:19: 17000000 INFO @ Tue, 02 Aug 2022 18:40:25: 15000000 INFO @ Tue, 02 Aug 2022 18:40:27: 10000000 INFO @ Tue, 02 Aug 2022 18:40:31: 18000000 INFO @ Tue, 02 Aug 2022 18:40:37: 16000000 INFO @ Tue, 02 Aug 2022 18:40:42: 11000000 INFO @ Tue, 02 Aug 2022 18:40:43: 19000000 INFO @ Tue, 02 Aug 2022 18:40:49: 17000000 INFO @ Tue, 02 Aug 2022 18:40:55: 20000000 INFO @ Tue, 02 Aug 2022 18:40:58: 12000000 INFO @ Tue, 02 Aug 2022 18:41:01: 18000000 INFO @ Tue, 02 Aug 2022 18:41:07: 21000000 INFO @ Tue, 02 Aug 2022 18:41:12: 13000000 INFO @ Tue, 02 Aug 2022 18:41:13: 19000000 INFO @ Tue, 02 Aug 2022 18:41:19: 22000000 INFO @ Tue, 02 Aug 2022 18:41:25: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:41:27: 14000000 INFO @ Tue, 02 Aug 2022 18:41:31: 23000000 INFO @ Tue, 02 Aug 2022 18:41:37: 21000000 INFO @ Tue, 02 Aug 2022 18:41:42: 15000000 INFO @ Tue, 02 Aug 2022 18:41:43: 24000000 INFO @ Tue, 02 Aug 2022 18:41:49: 22000000 INFO @ Tue, 02 Aug 2022 18:41:56: 25000000 INFO @ Tue, 02 Aug 2022 18:41:57: 16000000 INFO @ Tue, 02 Aug 2022 18:42:01: 23000000 INFO @ Tue, 02 Aug 2022 18:42:08: 26000000 INFO @ Tue, 02 Aug 2022 18:42:13: 17000000 INFO @ Tue, 02 Aug 2022 18:42:13: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:42:20: 27000000 INFO @ Tue, 02 Aug 2022 18:42:26: 25000000 INFO @ Tue, 02 Aug 2022 18:42:29: 18000000 INFO @ Tue, 02 Aug 2022 18:42:33: 28000000 INFO @ Tue, 02 Aug 2022 18:42:39: 26000000 INFO @ Tue, 02 Aug 2022 18:42:44: 19000000 INFO @ Tue, 02 Aug 2022 18:42:46: 29000000 INFO @ Tue, 02 Aug 2022 18:42:52: 27000000 INFO @ Tue, 02 Aug 2022 18:42:58: 30000000 INFO @ Tue, 02 Aug 2022 18:43:00: 20000000 INFO @ Tue, 02 Aug 2022 18:43:01: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:43:01: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:43:01: #1 total tags in treatment: 10446528 INFO @ Tue, 02 Aug 2022 18:43:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:43:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:43:01: #1 tags after filtering in treatment: 7439474 INFO @ Tue, 02 Aug 2022 18:43:01: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 18:43:01: #1 finished! INFO @ Tue, 02 Aug 2022 18:43:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:43:02: #2 number of paired peaks: 2463 INFO @ Tue, 02 Aug 2022 18:43:02: start model_add_line... INFO @ Tue, 02 Aug 2022 18:43:02: start X-correlation... INFO @ Tue, 02 Aug 2022 18:43:02: end of X-cor INFO @ Tue, 02 Aug 2022 18:43:02: #2 finished! INFO @ Tue, 02 Aug 2022 18:43:02: #2 predicted fragment length is 244 bps INFO @ Tue, 02 Aug 2022 18:43:02: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 02 Aug 2022 18:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.05_model.r WARNING @ Tue, 02 Aug 2022 18:43:02: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:43:02: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Tue, 02 Aug 2022 18:43:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:43:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:43:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:43:04: 28000000 INFO @ Tue, 02 Aug 2022 18:43:15: 21000000 INFO @ Tue, 02 Aug 2022 18:43:16: 29000000 INFO @ Tue, 02 Aug 2022 18:43:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:43:27: 30000000 INFO @ Tue, 02 Aug 2022 18:43:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:43:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:43:30: #1 total tags in treatment: 10446528 INFO @ Tue, 02 Aug 2022 18:43:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:43:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:43:30: 22000000 INFO @ Tue, 02 Aug 2022 18:43:30: #1 tags after filtering in treatment: 7439474 INFO @ Tue, 02 Aug 2022 18:43:30: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 18:43:30: #1 finished! INFO @ Tue, 02 Aug 2022 18:43:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.05_summits.bed INFO @ Tue, 02 Aug 2022 18:43:31: Done! INFO @ Tue, 02 Aug 2022 18:43:31: #2 number of paired peaks: 2463 INFO @ Tue, 02 Aug 2022 18:43:31: start model_add_line... INFO @ Tue, 02 Aug 2022 18:43:31: start X-correlation... INFO @ Tue, 02 Aug 2022 18:43:31: end of X-cor INFO @ Tue, 02 Aug 2022 18:43:31: #2 finished! INFO @ Tue, 02 Aug 2022 18:43:31: #2 predicted fragment length is 244 bps INFO @ Tue, 02 Aug 2022 18:43:31: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 02 Aug 2022 18:43:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.10_model.r WARNING @ Tue, 02 Aug 2022 18:43:31: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:43:31: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Tue, 02 Aug 2022 18:43:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:43:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:43:31: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8330 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:43:45: 23000000 INFO @ Tue, 02 Aug 2022 18:43:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.10_summits.bed INFO @ Tue, 02 Aug 2022 18:43:59: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5519 records, 4 fields): 72 millis INFO @ Tue, 02 Aug 2022 18:44:00: 24000000 CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:44:14: 25000000 INFO @ Tue, 02 Aug 2022 18:44:29: 26000000 INFO @ Tue, 02 Aug 2022 18:44:45: 27000000 INFO @ Tue, 02 Aug 2022 18:45:00: 28000000 INFO @ Tue, 02 Aug 2022 18:45:16: 29000000 INFO @ Tue, 02 Aug 2022 18:45:31: 30000000 INFO @ Tue, 02 Aug 2022 18:45:35: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:45:35: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:45:35: #1 total tags in treatment: 10446528 INFO @ Tue, 02 Aug 2022 18:45:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:45:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:45:35: #1 tags after filtering in treatment: 7439474 INFO @ Tue, 02 Aug 2022 18:45:35: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 18:45:35: #1 finished! INFO @ Tue, 02 Aug 2022 18:45:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:45:35: #2 number of paired peaks: 2463 INFO @ Tue, 02 Aug 2022 18:45:35: start model_add_line... INFO @ Tue, 02 Aug 2022 18:45:36: start X-correlation... INFO @ Tue, 02 Aug 2022 18:45:36: end of X-cor INFO @ Tue, 02 Aug 2022 18:45:36: #2 finished! INFO @ Tue, 02 Aug 2022 18:45:36: #2 predicted fragment length is 244 bps INFO @ Tue, 02 Aug 2022 18:45:36: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 02 Aug 2022 18:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.20_model.r WARNING @ Tue, 02 Aug 2022 18:45:36: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:45:36: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Tue, 02 Aug 2022 18:45:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:45:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:45:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:45:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:46:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:46:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:46:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175825/SRX12175825.20_summits.bed INFO @ Tue, 02 Aug 2022 18:46:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2728 records, 4 fields): 18 millis CompletedMACS2peakCalling