Job ID = 14171471 SRX = SRX10971109 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:45:53 prefetch.2.10.7: 1) Downloading 'SRR14631233'... 2021-12-11T02:45:53 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:47:04 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:47:04 prefetch.2.10.7: 1) 'SRR14631233' was downloaded successfully 2021-12-11T02:47:04 prefetch.2.10.7: 'SRR14631233' has 0 unresolved dependencies Read 16531737 spots for SRR14631233/SRR14631233.sra Written 16531737 spots for SRR14631233/SRR14631233.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172156 ("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: 00:53:29 16531737 reads; of these: 16531737 (100.00%) were paired; of these: 1861135 (11.26%) aligned concordantly 0 times 12314215 (74.49%) aligned concordantly exactly 1 time 2356387 (14.25%) aligned concordantly >1 times ---- 1861135 pairs aligned concordantly 0 times; of these: 151707 (8.15%) aligned discordantly 1 time ---- 1709428 pairs aligned 0 times concordantly or discordantly; of these: 3418856 mates make up the pairs; of these: 2115919 (61.89%) aligned 0 times 668345 (19.55%) aligned exactly 1 time 634592 (18.56%) aligned >1 times 93.60% overall alignment rate Time searching: 00:53:29 Overall time: 00:53:29 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 16 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] 2202634 / 14578968 = 0.1511 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 12:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.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 12:53:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:53:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:53:59: 1000000 INFO @ Sat, 11 Dec 2021 12:54:06: 2000000 INFO @ Sat, 11 Dec 2021 12:54:13: 3000000 INFO @ Sat, 11 Dec 2021 12:54:20: 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 @ Sat, 11 Dec 2021 12:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.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 12:54:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:54:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:54:27: 5000000 INFO @ Sat, 11 Dec 2021 12:54:30: 1000000 INFO @ Sat, 11 Dec 2021 12:54:34: 6000000 INFO @ Sat, 11 Dec 2021 12:54:38: 2000000 INFO @ Sat, 11 Dec 2021 12:54:42: 7000000 INFO @ Sat, 11 Dec 2021 12:54:46: 3000000 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 12:54:50: 8000000 INFO @ Sat, 11 Dec 2021 12:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.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 12:54:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:54:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:54:54: 4000000 INFO @ Sat, 11 Dec 2021 12:54:59: 1000000 INFO @ Sat, 11 Dec 2021 12:54:59: 9000000 INFO @ Sat, 11 Dec 2021 12:55:02: 5000000 INFO @ Sat, 11 Dec 2021 12:55:05: 2000000 INFO @ Sat, 11 Dec 2021 12:55:07: 10000000 INFO @ Sat, 11 Dec 2021 12:55:11: 6000000 INFO @ Sat, 11 Dec 2021 12:55:12: 3000000 INFO @ Sat, 11 Dec 2021 12:55:15: 11000000 INFO @ Sat, 11 Dec 2021 12:55:19: 4000000 INFO @ Sat, 11 Dec 2021 12:55:19: 7000000 INFO @ Sat, 11 Dec 2021 12:55:24: 12000000 INFO @ Sat, 11 Dec 2021 12:55:25: 5000000 INFO @ Sat, 11 Dec 2021 12:55:27: 8000000 INFO @ Sat, 11 Dec 2021 12:55:32: 6000000 INFO @ Sat, 11 Dec 2021 12:55:32: 13000000 INFO @ Sat, 11 Dec 2021 12:55:36: 9000000 INFO @ Sat, 11 Dec 2021 12:55:39: 7000000 INFO @ Sat, 11 Dec 2021 12:55:40: 14000000 INFO @ Sat, 11 Dec 2021 12:55:44: 10000000 INFO @ Sat, 11 Dec 2021 12:55:45: 8000000 INFO @ Sat, 11 Dec 2021 12:55:49: 15000000 INFO @ Sat, 11 Dec 2021 12:55:52: 9000000 INFO @ Sat, 11 Dec 2021 12:55:52: 11000000 INFO @ Sat, 11 Dec 2021 12:55:57: 16000000 INFO @ Sat, 11 Dec 2021 12:55:59: 10000000 INFO @ Sat, 11 Dec 2021 12:56:01: 12000000 INFO @ Sat, 11 Dec 2021 12:56:05: 11000000 INFO @ Sat, 11 Dec 2021 12:56:05: 17000000 INFO @ Sat, 11 Dec 2021 12:56:09: 13000000 INFO @ Sat, 11 Dec 2021 12:56:12: 12000000 INFO @ Sat, 11 Dec 2021 12:56:13: 18000000 INFO @ Sat, 11 Dec 2021 12:56:17: 14000000 INFO @ Sat, 11 Dec 2021 12:56:18: 13000000 INFO @ Sat, 11 Dec 2021 12:56:22: 19000000 INFO @ Sat, 11 Dec 2021 12:56:25: 14000000 INFO @ Sat, 11 Dec 2021 12:56:25: 15000000 INFO @ Sat, 11 Dec 2021 12:56:30: 20000000 INFO @ Sat, 11 Dec 2021 12:56:31: 15000000 INFO @ Sat, 11 Dec 2021 12:56:34: 16000000 INFO @ Sat, 11 Dec 2021 12:56:38: 16000000 INFO @ Sat, 11 Dec 2021 12:56:39: 21000000 INFO @ Sat, 11 Dec 2021 12:56:42: 17000000 INFO @ Sat, 11 Dec 2021 12:56:45: 17000000 INFO @ Sat, 11 Dec 2021 12:56:47: 22000000 INFO @ Sat, 11 Dec 2021 12:56:50: 18000000 INFO @ Sat, 11 Dec 2021 12:56:52: 18000000 INFO @ Sat, 11 Dec 2021 12:56:55: 23000000 INFO @ Sat, 11 Dec 2021 12:56:59: 19000000 INFO @ Sat, 11 Dec 2021 12:56:59: 19000000 INFO @ Sat, 11 Dec 2021 12:57:03: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:57:07: 20000000 INFO @ Sat, 11 Dec 2021 12:57:08: 20000000 INFO @ Sat, 11 Dec 2021 12:57:12: 25000000 INFO @ Sat, 11 Dec 2021 12:57:16: 21000000 INFO @ Sat, 11 Dec 2021 12:57:16: 21000000 INFO @ Sat, 11 Dec 2021 12:57:20: 26000000 INFO @ Sat, 11 Dec 2021 12:57:23: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:57:23: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:57:23: #1 total tags in treatment: 12478651 INFO @ Sat, 11 Dec 2021 12:57:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:57:23: #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 12:57:24: #1 tags after filtering in treatment: 11939174 INFO @ Sat, 11 Dec 2021 12:57:24: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 12:57:24: #1 finished! INFO @ Sat, 11 Dec 2021 12:57:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:57:24: 22000000 INFO @ Sat, 11 Dec 2021 12:57:24: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 12:57:24: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 12:57:24: start model_add_line... INFO @ Sat, 11 Dec 2021 12:57:25: start X-correlation... INFO @ Sat, 11 Dec 2021 12:57:25: end of X-cor INFO @ Sat, 11 Dec 2021 12:57:25: #2 finished! INFO @ Sat, 11 Dec 2021 12:57:25: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 12:57:25: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 11 Dec 2021 12:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.05_model.r INFO @ Sat, 11 Dec 2021 12:57:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:57:25: 22000000 INFO @ Sat, 11 Dec 2021 12:57:32: 23000000 INFO @ Sat, 11 Dec 2021 12:57:33: 23000000 INFO @ Sat, 11 Dec 2021 12:57:40: 24000000 INFO @ Sat, 11 Dec 2021 12:57:41: 24000000 INFO @ Sat, 11 Dec 2021 12:57:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:57:49: 25000000 INFO @ Sat, 11 Dec 2021 12:57:49: 25000000 INFO @ Sat, 11 Dec 2021 12:57:56: 26000000 INFO @ Sat, 11 Dec 2021 12:57:58: 26000000 INFO @ Sat, 11 Dec 2021 12:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.05_summits.bed INFO @ Sat, 11 Dec 2021 12:58:00: Done! INFO @ Sat, 11 Dec 2021 12:58:00: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:58:00: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:58:00: #1 total tags in treatment: 12478651 INFO @ Sat, 11 Dec 2021 12:58:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:58:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (934 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:58:00: #1 tags after filtering in treatment: 11939174 INFO @ Sat, 11 Dec 2021 12:58:00: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 12:58:00: #1 finished! INFO @ Sat, 11 Dec 2021 12:58:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:58:01: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 12:58:01: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 12:58:01: start model_add_line... INFO @ Sat, 11 Dec 2021 12:58:01: start X-correlation... INFO @ Sat, 11 Dec 2021 12:58:01: end of X-cor INFO @ Sat, 11 Dec 2021 12:58:01: #2 finished! INFO @ Sat, 11 Dec 2021 12:58:01: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 12:58:01: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 11 Dec 2021 12:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.10_model.r BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:58:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:58:02: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 12:58:02: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 12:58:02: #1 total tags in treatment: 12478651 INFO @ Sat, 11 Dec 2021 12:58:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:58:02: #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 12:58:02: #1 tags after filtering in treatment: 11939174 INFO @ Sat, 11 Dec 2021 12:58:02: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 12:58:02: #1 finished! INFO @ Sat, 11 Dec 2021 12:58:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:58:03: #2 number of paired peaks: 264 WARNING @ Sat, 11 Dec 2021 12:58:03: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 11 Dec 2021 12:58:03: start model_add_line... INFO @ Sat, 11 Dec 2021 12:58:03: start X-correlation... INFO @ Sat, 11 Dec 2021 12:58:03: end of X-cor INFO @ Sat, 11 Dec 2021 12:58:03: #2 finished! INFO @ Sat, 11 Dec 2021 12:58:03: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 12:58:03: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 11 Dec 2021 12:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.20_model.r INFO @ Sat, 11 Dec 2021 12:58:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:58:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:58:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:58:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.10_summits.bed INFO @ Sat, 11 Dec 2021 12:58:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (714 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:58:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971109/SRX10971109.20_summits.bed INFO @ Sat, 11 Dec 2021 12:58:38: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (504 records, 4 fields): 20 millis CompletedMACS2peakCalling