Job ID = 6627021 SRX = SRX8325347 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:25:58 prefetch.2.10.7: 1) Downloading 'SRR11772153'... 2020-07-14T00:25:58 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:27:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:27:46 prefetch.2.10.7: 1) 'SRR11772153' was downloaded successfully 2020-07-14T00:27:46 prefetch.2.10.7: 'SRR11772153' has 0 unresolved dependencies Read 9690076 spots for SRR11772153/SRR11772153.sra Written 9690076 spots for SRR11772153/SRR11772153.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627304 ("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: 00:32:29 9690076 reads; of these: 9690076 (100.00%) were paired; of these: 3156206 (32.57%) aligned concordantly 0 times 4778162 (49.31%) aligned concordantly exactly 1 time 1755708 (18.12%) aligned concordantly >1 times ---- 3156206 pairs aligned concordantly 0 times; of these: 1331307 (42.18%) aligned discordantly 1 time ---- 1824899 pairs aligned 0 times concordantly or discordantly; of these: 3649798 mates make up the pairs; of these: 1776445 (48.67%) aligned 0 times 1053927 (28.88%) aligned exactly 1 time 819426 (22.45%) aligned >1 times 90.83% overall alignment rate Time searching: 00:32:29 Overall time: 00:32:29 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] 2295949 / 7592640 = 0.3024 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:09:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.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, 14 Jul 2020 10:09:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:09:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:09:46: 1000000 INFO @ Tue, 14 Jul 2020 10:09:53: 2000000 INFO @ Tue, 14 Jul 2020 10:10:00: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:10:08: 4000000 INFO @ Tue, 14 Jul 2020 10:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.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, 14 Jul 2020 10:10:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:10:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:10:15: 5000000 INFO @ Tue, 14 Jul 2020 10:10:16: 1000000 INFO @ Tue, 14 Jul 2020 10:10:23: 6000000 INFO @ Tue, 14 Jul 2020 10:10:25: 2000000 INFO @ Tue, 14 Jul 2020 10:10:31: 7000000 INFO @ Tue, 14 Jul 2020 10:10:34: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.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, 14 Jul 2020 10:10:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:10:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:10:39: 8000000 INFO @ Tue, 14 Jul 2020 10:10:44: 4000000 INFO @ Tue, 14 Jul 2020 10:10:46: 1000000 INFO @ Tue, 14 Jul 2020 10:10:46: 9000000 INFO @ Tue, 14 Jul 2020 10:10:53: 5000000 INFO @ Tue, 14 Jul 2020 10:10:54: 10000000 INFO @ Tue, 14 Jul 2020 10:10:54: 2000000 INFO @ Tue, 14 Jul 2020 10:11:02: 11000000 INFO @ Tue, 14 Jul 2020 10:11:02: 3000000 INFO @ Tue, 14 Jul 2020 10:11:02: 6000000 INFO @ Tue, 14 Jul 2020 10:11:10: 12000000 INFO @ Tue, 14 Jul 2020 10:11:10: 4000000 INFO @ Tue, 14 Jul 2020 10:11:11: 7000000 INFO @ Tue, 14 Jul 2020 10:11:18: 13000000 INFO @ Tue, 14 Jul 2020 10:11:18: #1 tag size is determined as 145 bps INFO @ Tue, 14 Jul 2020 10:11:18: #1 tag size = 145 INFO @ Tue, 14 Jul 2020 10:11:18: #1 total tags in treatment: 4526374 INFO @ Tue, 14 Jul 2020 10:11:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:11:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:11:18: #1 tags after filtering in treatment: 3966205 INFO @ Tue, 14 Jul 2020 10:11:18: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 14 Jul 2020 10:11:18: #1 finished! INFO @ Tue, 14 Jul 2020 10:11:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:11:18: #2 number of paired peaks: 3021 INFO @ Tue, 14 Jul 2020 10:11:18: start model_add_line... INFO @ Tue, 14 Jul 2020 10:11:18: start X-correlation... INFO @ Tue, 14 Jul 2020 10:11:18: end of X-cor INFO @ Tue, 14 Jul 2020 10:11:18: #2 finished! INFO @ Tue, 14 Jul 2020 10:11:18: #2 predicted fragment length is 256 bps INFO @ Tue, 14 Jul 2020 10:11:18: #2 alternative fragment length(s) may be 256 bps INFO @ Tue, 14 Jul 2020 10:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.05_model.r WARNING @ Tue, 14 Jul 2020 10:11:18: #2 Since the d (256) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:11:18: #2 You may need to consider one of the other alternative d(s): 256 WARNING @ Tue, 14 Jul 2020 10:11:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:11:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:11:18: 5000000 INFO @ Tue, 14 Jul 2020 10:11:19: 8000000 INFO @ Tue, 14 Jul 2020 10:11:26: 6000000 INFO @ Tue, 14 Jul 2020 10:11:27: 9000000 INFO @ Tue, 14 Jul 2020 10:11:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.05_summits.bed INFO @ Tue, 14 Jul 2020 10:11:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7837 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:11:34: 7000000 INFO @ Tue, 14 Jul 2020 10:11:36: 10000000 INFO @ Tue, 14 Jul 2020 10:11:42: 8000000 INFO @ Tue, 14 Jul 2020 10:11:45: 11000000 INFO @ Tue, 14 Jul 2020 10:11:50: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:11:54: 12000000 INFO @ Tue, 14 Jul 2020 10:11:58: 10000000 INFO @ Tue, 14 Jul 2020 10:12:03: 13000000 INFO @ Tue, 14 Jul 2020 10:12:03: #1 tag size is determined as 145 bps INFO @ Tue, 14 Jul 2020 10:12:03: #1 tag size = 145 INFO @ Tue, 14 Jul 2020 10:12:03: #1 total tags in treatment: 4526374 INFO @ Tue, 14 Jul 2020 10:12:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:12:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:12:03: #1 tags after filtering in treatment: 3966205 INFO @ Tue, 14 Jul 2020 10:12:03: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 14 Jul 2020 10:12:03: #1 finished! INFO @ Tue, 14 Jul 2020 10:12:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:12:03: #2 number of paired peaks: 3021 INFO @ Tue, 14 Jul 2020 10:12:03: start model_add_line... INFO @ Tue, 14 Jul 2020 10:12:03: start X-correlation... INFO @ Tue, 14 Jul 2020 10:12:03: end of X-cor INFO @ Tue, 14 Jul 2020 10:12:03: #2 finished! INFO @ Tue, 14 Jul 2020 10:12:03: #2 predicted fragment length is 256 bps INFO @ Tue, 14 Jul 2020 10:12:03: #2 alternative fragment length(s) may be 256 bps INFO @ Tue, 14 Jul 2020 10:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.10_model.r WARNING @ Tue, 14 Jul 2020 10:12:03: #2 Since the d (256) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:12:03: #2 You may need to consider one of the other alternative d(s): 256 WARNING @ Tue, 14 Jul 2020 10:12:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:12:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:12:06: 11000000 INFO @ Tue, 14 Jul 2020 10:12:14: 12000000 INFO @ Tue, 14 Jul 2020 10:12:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.10_summits.bed INFO @ Tue, 14 Jul 2020 10:12:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4312 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:12:22: 13000000 INFO @ Tue, 14 Jul 2020 10:12:22: #1 tag size is determined as 145 bps INFO @ Tue, 14 Jul 2020 10:12:22: #1 tag size = 145 INFO @ Tue, 14 Jul 2020 10:12:22: #1 total tags in treatment: 4526374 INFO @ Tue, 14 Jul 2020 10:12:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:12:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:12:22: #1 tags after filtering in treatment: 3966205 INFO @ Tue, 14 Jul 2020 10:12:22: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 14 Jul 2020 10:12:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:12:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:12:22: #2 number of paired peaks: 3021 INFO @ Tue, 14 Jul 2020 10:12:22: start model_add_line... INFO @ Tue, 14 Jul 2020 10:12:22: start X-correlation... INFO @ Tue, 14 Jul 2020 10:12:22: end of X-cor INFO @ Tue, 14 Jul 2020 10:12:22: #2 finished! INFO @ Tue, 14 Jul 2020 10:12:22: #2 predicted fragment length is 256 bps INFO @ Tue, 14 Jul 2020 10:12:22: #2 alternative fragment length(s) may be 256 bps INFO @ Tue, 14 Jul 2020 10:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.20_model.r WARNING @ Tue, 14 Jul 2020 10:12:23: #2 Since the d (256) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:12:23: #2 You may need to consider one of the other alternative d(s): 256 WARNING @ Tue, 14 Jul 2020 10:12:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:12:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:12:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:12:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:12:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325347/SRX8325347.20_summits.bed INFO @ Tue, 14 Jul 2020 10:12:37: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1986 records, 4 fields): 4 millis CompletedMACS2peakCalling