Job ID = 14172159 SRX = SRX9786717 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15685627 spots for SRR13362636/SRR13362636.sra Written 15685627 spots for SRR13362636/SRR13362636.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172665 ("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: 00:15:36 15685627 reads; of these: 15685627 (100.00%) were paired; of these: 3773182 (24.06%) aligned concordantly 0 times 7301047 (46.55%) aligned concordantly exactly 1 time 4611398 (29.40%) aligned concordantly >1 times ---- 3773182 pairs aligned concordantly 0 times; of these: 928471 (24.61%) aligned discordantly 1 time ---- 2844711 pairs aligned 0 times concordantly or discordantly; of these: 5689422 mates make up the pairs; of these: 4530679 (79.63%) aligned 0 times 455773 (8.01%) aligned exactly 1 time 702970 (12.36%) aligned >1 times 85.56% overall alignment rate Time searching: 00:15:36 Overall time: 00:15:36 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] 3061896 / 12742413 = 0.2403 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 14:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.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 14:54:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:54:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:54:42: 1000000 INFO @ Sat, 11 Dec 2021 14:54:47: 2000000 INFO @ Sat, 11 Dec 2021 14:54:52: 3000000 INFO @ Sat, 11 Dec 2021 14:54:58: 4000000 INFO @ Sat, 11 Dec 2021 14:55:03: 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 14:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.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 14:55:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:09: 6000000 INFO @ Sat, 11 Dec 2021 14:55:12: 1000000 INFO @ Sat, 11 Dec 2021 14:55:14: 7000000 INFO @ Sat, 11 Dec 2021 14:55:17: 2000000 INFO @ Sat, 11 Dec 2021 14:55:19: 8000000 INFO @ Sat, 11 Dec 2021 14:55:22: 3000000 INFO @ Sat, 11 Dec 2021 14:55:24: 9000000 INFO @ Sat, 11 Dec 2021 14:55:27: 4000000 INFO @ Sat, 11 Dec 2021 14:55:30: 10000000 INFO @ Sat, 11 Dec 2021 14:55:32: 5000000 INFO @ Sat, 11 Dec 2021 14:55:35: 11000000 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 14:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.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 14:55:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:37: 6000000 INFO @ Sat, 11 Dec 2021 14:55:40: 12000000 INFO @ Sat, 11 Dec 2021 14:55:42: 1000000 INFO @ Sat, 11 Dec 2021 14:55:43: 7000000 INFO @ Sat, 11 Dec 2021 14:55:45: 13000000 INFO @ Sat, 11 Dec 2021 14:55:47: 2000000 INFO @ Sat, 11 Dec 2021 14:55:48: 8000000 INFO @ Sat, 11 Dec 2021 14:55:51: 14000000 INFO @ Sat, 11 Dec 2021 14:55:52: 3000000 INFO @ Sat, 11 Dec 2021 14:55:54: 9000000 INFO @ Sat, 11 Dec 2021 14:55:56: 15000000 INFO @ Sat, 11 Dec 2021 14:55:57: 4000000 INFO @ Sat, 11 Dec 2021 14:55:59: 10000000 INFO @ Sat, 11 Dec 2021 14:56:01: 16000000 INFO @ Sat, 11 Dec 2021 14:56:02: 5000000 INFO @ Sat, 11 Dec 2021 14:56:04: 11000000 INFO @ Sat, 11 Dec 2021 14:56:06: 17000000 INFO @ Sat, 11 Dec 2021 14:56:08: 6000000 INFO @ Sat, 11 Dec 2021 14:56:10: 12000000 INFO @ Sat, 11 Dec 2021 14:56:11: 18000000 INFO @ Sat, 11 Dec 2021 14:56:13: 7000000 INFO @ Sat, 11 Dec 2021 14:56:15: 13000000 INFO @ Sat, 11 Dec 2021 14:56:17: 19000000 INFO @ Sat, 11 Dec 2021 14:56:19: 8000000 INFO @ Sat, 11 Dec 2021 14:56:20: 14000000 INFO @ Sat, 11 Dec 2021 14:56:22: 20000000 INFO @ Sat, 11 Dec 2021 14:56:24: 9000000 INFO @ Sat, 11 Dec 2021 14:56:25: 15000000 INFO @ Sat, 11 Dec 2021 14:56:26: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:56:26: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:56:26: #1 total tags in treatment: 8898787 INFO @ Sat, 11 Dec 2021 14:56:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:56:26: #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 14:56:26: #1 tags after filtering in treatment: 7039928 INFO @ Sat, 11 Dec 2021 14:56:26: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:56:26: #1 finished! INFO @ Sat, 11 Dec 2021 14:56:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:56:26: #2 number of paired peaks: 1509 INFO @ Sat, 11 Dec 2021 14:56:26: start model_add_line... INFO @ Sat, 11 Dec 2021 14:56:26: start X-correlation... INFO @ Sat, 11 Dec 2021 14:56:26: end of X-cor INFO @ Sat, 11 Dec 2021 14:56:26: #2 finished! INFO @ Sat, 11 Dec 2021 14:56:26: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 14:56:26: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 14:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.05_model.r WARNING @ Sat, 11 Dec 2021 14:56:26: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:56:26: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 11 Dec 2021 14:56:26: #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 14:56:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:56:30: 10000000 INFO @ Sat, 11 Dec 2021 14:56:31: 16000000 INFO @ Sat, 11 Dec 2021 14:56:35: 11000000 INFO @ Sat, 11 Dec 2021 14:56:36: 17000000 INFO @ Sat, 11 Dec 2021 14:56:41: 12000000 INFO @ Sat, 11 Dec 2021 14:56:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:56:42: 18000000 INFO @ Sat, 11 Dec 2021 14:56:46: 13000000 INFO @ Sat, 11 Dec 2021 14:56:47: 19000000 INFO @ Sat, 11 Dec 2021 14:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.05_summits.bed INFO @ Sat, 11 Dec 2021 14:56:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7218 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:56:51: 14000000 INFO @ Sat, 11 Dec 2021 14:56:52: 20000000 INFO @ Sat, 11 Dec 2021 14:56:56: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:56:56: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:56:56: #1 total tags in treatment: 8898787 INFO @ Sat, 11 Dec 2021 14:56:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:56:56: #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 14:56:56: #1 tags after filtering in treatment: 7039928 INFO @ Sat, 11 Dec 2021 14:56:56: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:56:56: #1 finished! INFO @ Sat, 11 Dec 2021 14:56:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:56:56: 15000000 INFO @ Sat, 11 Dec 2021 14:56:57: #2 number of paired peaks: 1509 INFO @ Sat, 11 Dec 2021 14:56:57: start model_add_line... BedGraph に変換しました。 INFO @ Sat, 11 Dec 2021 14:56:57: start X-correlation... BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:56:57: end of X-cor INFO @ Sat, 11 Dec 2021 14:56:57: #2 finished! INFO @ Sat, 11 Dec 2021 14:56:57: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 14:56:57: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 14:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.10_model.r WARNING @ Sat, 11 Dec 2021 14:56:57: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:56:57: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 11 Dec 2021 14:56:57: #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 14:56:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:57:02: 16000000 INFO @ Sat, 11 Dec 2021 14:57:07: 17000000 INFO @ Sat, 11 Dec 2021 14:57:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:57:12: 18000000 INFO @ Sat, 11 Dec 2021 14:57:17: 19000000 INFO @ Sat, 11 Dec 2021 14:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.10_summits.bed INFO @ Sat, 11 Dec 2021 14:57:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3671 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:57:22: 20000000 INFO @ Sat, 11 Dec 2021 14:57:26: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 14:57:26: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 14:57:26: #1 total tags in treatment: 8898787 INFO @ Sat, 11 Dec 2021 14:57:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:57:26: #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 14:57:26: #1 tags after filtering in treatment: 7039928 INFO @ Sat, 11 Dec 2021 14:57:26: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 14:57:26: #1 finished! INFO @ Sat, 11 Dec 2021 14:57:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:57:26: #2 number of paired peaks: 1509 INFO @ Sat, 11 Dec 2021 14:57:26: start model_add_line... INFO @ Sat, 11 Dec 2021 14:57:26: start X-correlation... INFO @ Sat, 11 Dec 2021 14:57:26: end of X-cor INFO @ Sat, 11 Dec 2021 14:57:26: #2 finished! INFO @ Sat, 11 Dec 2021 14:57:26: #2 predicted fragment length is 95 bps INFO @ Sat, 11 Dec 2021 14:57:26: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 11 Dec 2021 14:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.20_model.r WARNING @ Sat, 11 Dec 2021 14:57:26: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:57:26: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 11 Dec 2021 14:57:26: #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 14:57:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:57:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:57:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:57:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:57:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9786717/SRX9786717.20_summits.bed INFO @ Sat, 11 Dec 2021 14:57:48: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (864 records, 4 fields): 388 millis CompletedMACS2peakCalling