Job ID = 6627094 SRX = SRX8347290 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:50:45 prefetch.2.10.7: 1) Downloading 'SRR11795473'... 2020-07-14T00:50:45 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:54:09 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:54:09 prefetch.2.10.7: 1) 'SRR11795473' was downloaded successfully 2020-07-14T00:54:09 prefetch.2.10.7: 'SRR11795473' has 0 unresolved dependencies Read 9025516 spots for SRR11795473/SRR11795473.sra Written 9025516 spots for SRR11795473/SRR11795473.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627325 ("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: 00:14:40 9025516 reads; of these: 9025516 (100.00%) were paired; of these: 4903315 (54.33%) aligned concordantly 0 times 3359092 (37.22%) aligned concordantly exactly 1 time 763109 (8.46%) aligned concordantly >1 times ---- 4903315 pairs aligned concordantly 0 times; of these: 309869 (6.32%) aligned discordantly 1 time ---- 4593446 pairs aligned 0 times concordantly or discordantly; of these: 9186892 mates make up the pairs; of these: 8905192 (96.93%) aligned 0 times 110464 (1.20%) aligned exactly 1 time 171236 (1.86%) aligned >1 times 50.67% overall alignment rate Time searching: 00:14:40 Overall time: 00:14:40 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 8 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] 2825948 / 4413402 = 0.6403 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 10:13:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.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 10:13:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:13:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:13:19: 1000000 INFO @ Tue, 14 Jul 2020 10:13:27: 2000000 INFO @ Tue, 14 Jul 2020 10:13:34: 3000000 INFO @ Tue, 14 Jul 2020 10:13:38: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:13:38: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:13:38: #1 total tags in treatment: 1421381 INFO @ Tue, 14 Jul 2020 10:13:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:13:38: #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 10:13:38: #1 tags after filtering in treatment: 1389646 INFO @ Tue, 14 Jul 2020 10:13:38: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:13:38: #1 finished! INFO @ Tue, 14 Jul 2020 10:13:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:13:38: #2 number of paired peaks: 958 WARNING @ Tue, 14 Jul 2020 10:13:38: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Tue, 14 Jul 2020 10:13:38: start model_add_line... INFO @ Tue, 14 Jul 2020 10:13:38: start X-correlation... INFO @ Tue, 14 Jul 2020 10:13:38: end of X-cor INFO @ Tue, 14 Jul 2020 10:13:38: #2 finished! INFO @ Tue, 14 Jul 2020 10:13:38: #2 predicted fragment length is 196 bps INFO @ Tue, 14 Jul 2020 10:13:38: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 14 Jul 2020 10:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.05_model.r WARNING @ Tue, 14 Jul 2020 10:13:38: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:13:38: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 14 Jul 2020 10:13:38: #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 10:13:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:13:38: #3 Pre-compute pvalue-qvalue table... 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 10:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.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 10:13:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:13:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:13:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.05_summits.bed INFO @ Tue, 14 Jul 2020 10:13:43: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1211 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:13:49: 1000000 INFO @ Tue, 14 Jul 2020 10:13:56: 2000000 INFO @ Tue, 14 Jul 2020 10:14:03: 3000000 INFO @ Tue, 14 Jul 2020 10:14:06: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:14:06: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:14:06: #1 total tags in treatment: 1421381 INFO @ Tue, 14 Jul 2020 10:14:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:14:06: #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 10:14:06: #1 tags after filtering in treatment: 1389646 INFO @ Tue, 14 Jul 2020 10:14:06: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:14:06: #1 finished! INFO @ Tue, 14 Jul 2020 10:14:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:14:06: #2 number of paired peaks: 958 WARNING @ Tue, 14 Jul 2020 10:14:06: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Tue, 14 Jul 2020 10:14:06: start model_add_line... INFO @ Tue, 14 Jul 2020 10:14:06: start X-correlation... INFO @ Tue, 14 Jul 2020 10:14:06: end of X-cor INFO @ Tue, 14 Jul 2020 10:14:06: #2 finished! INFO @ Tue, 14 Jul 2020 10:14:06: #2 predicted fragment length is 196 bps INFO @ Tue, 14 Jul 2020 10:14:06: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 14 Jul 2020 10:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.10_model.r WARNING @ Tue, 14 Jul 2020 10:14:06: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:14:06: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 14 Jul 2020 10:14:06: #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 10:14:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:14:06: #3 Pre-compute pvalue-qvalue table... 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 10:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.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 10:14:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:14:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:14:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:14:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:14:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.10_summits.bed INFO @ Tue, 14 Jul 2020 10:14:11: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:14:17: 1000000 INFO @ Tue, 14 Jul 2020 10:14:24: 2000000 INFO @ Tue, 14 Jul 2020 10:14:30: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:14:34: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:14:34: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:14:34: #1 total tags in treatment: 1421381 INFO @ Tue, 14 Jul 2020 10:14:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:14:34: #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 10:14:34: #1 tags after filtering in treatment: 1389646 INFO @ Tue, 14 Jul 2020 10:14:34: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:14:34: #1 finished! INFO @ Tue, 14 Jul 2020 10:14:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:14:34: #2 number of paired peaks: 958 WARNING @ Tue, 14 Jul 2020 10:14:34: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Tue, 14 Jul 2020 10:14:34: start model_add_line... INFO @ Tue, 14 Jul 2020 10:14:34: start X-correlation... INFO @ Tue, 14 Jul 2020 10:14:34: end of X-cor INFO @ Tue, 14 Jul 2020 10:14:34: #2 finished! INFO @ Tue, 14 Jul 2020 10:14:34: #2 predicted fragment length is 196 bps INFO @ Tue, 14 Jul 2020 10:14:34: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 14 Jul 2020 10:14:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.20_model.r WARNING @ Tue, 14 Jul 2020 10:14:34: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:14:34: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 14 Jul 2020 10:14:34: #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 10:14:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:14:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:14:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347290/SRX8347290.20_summits.bed INFO @ Tue, 14 Jul 2020 10:14:39: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。