Job ID = 6627046 SRX = SRX8325352 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5343689 spots for SRR11772158/SRR11772158.sra Written 5343689 spots for SRR11772158/SRR11772158.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627285 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:45 5343689 reads; of these: 5343689 (100.00%) were paired; of these: 1527145 (28.58%) aligned concordantly 0 times 2959246 (55.38%) aligned concordantly exactly 1 time 857298 (16.04%) aligned concordantly >1 times ---- 1527145 pairs aligned concordantly 0 times; of these: 544825 (35.68%) aligned discordantly 1 time ---- 982320 pairs aligned 0 times concordantly or discordantly; of these: 1964640 mates make up the pairs; of these: 1082402 (55.09%) aligned 0 times 480438 (24.45%) aligned exactly 1 time 401800 (20.45%) aligned >1 times 89.87% overall alignment rate Time searching: 00:15:46 Overall time: 00:15:46 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] 1488094 / 4199989 = 0.3543 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 09:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.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 09:57:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:57:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:57:16: 1000000 INFO @ Tue, 14 Jul 2020 09:57:26: 2000000 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 09:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.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 09:57:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:57:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:57:37: 3000000 INFO @ Tue, 14 Jul 2020 09:57:47: 1000000 INFO @ Tue, 14 Jul 2020 09:57:48: 4000000 INFO @ Tue, 14 Jul 2020 09:57:58: 2000000 INFO @ Tue, 14 Jul 2020 09:58:00: 5000000 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 09:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.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 09:58:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:58:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:58:09: 3000000 INFO @ Tue, 14 Jul 2020 09:58:12: 6000000 INFO @ Tue, 14 Jul 2020 09:58:17: 1000000 INFO @ Tue, 14 Jul 2020 09:58:20: #1 tag size is determined as 146 bps INFO @ Tue, 14 Jul 2020 09:58:20: #1 tag size = 146 INFO @ Tue, 14 Jul 2020 09:58:20: #1 total tags in treatment: 2479260 INFO @ Tue, 14 Jul 2020 09:58:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:58:20: #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 09:58:20: #1 tags after filtering in treatment: 2334421 INFO @ Tue, 14 Jul 2020 09:58:20: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 09:58:20: #1 finished! INFO @ Tue, 14 Jul 2020 09:58:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:58:20: #2 number of paired peaks: 1766 INFO @ Tue, 14 Jul 2020 09:58:20: start model_add_line... INFO @ Tue, 14 Jul 2020 09:58:20: start X-correlation... INFO @ Tue, 14 Jul 2020 09:58:20: end of X-cor INFO @ Tue, 14 Jul 2020 09:58:20: #2 finished! INFO @ Tue, 14 Jul 2020 09:58:20: #2 predicted fragment length is 231 bps INFO @ Tue, 14 Jul 2020 09:58:20: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 14 Jul 2020 09:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.05_model.r WARNING @ Tue, 14 Jul 2020 09:58:20: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:58:20: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Tue, 14 Jul 2020 09:58:20: #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 09:58:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:58:21: 4000000 INFO @ Tue, 14 Jul 2020 09:58:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.05_summits.bed INFO @ Tue, 14 Jul 2020 09:58:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2591 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:58:28: 2000000 INFO @ Tue, 14 Jul 2020 09:58:31: 5000000 INFO @ Tue, 14 Jul 2020 09:58:39: 3000000 INFO @ Tue, 14 Jul 2020 09:58:42: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:58:49: #1 tag size is determined as 146 bps INFO @ Tue, 14 Jul 2020 09:58:49: #1 tag size = 146 INFO @ Tue, 14 Jul 2020 09:58:49: #1 total tags in treatment: 2479260 INFO @ Tue, 14 Jul 2020 09:58:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:58:49: #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 09:58:49: #1 tags after filtering in treatment: 2334421 INFO @ Tue, 14 Jul 2020 09:58:49: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 09:58:49: #1 finished! INFO @ Tue, 14 Jul 2020 09:58:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:58:49: #2 number of paired peaks: 1766 INFO @ Tue, 14 Jul 2020 09:58:49: start model_add_line... INFO @ Tue, 14 Jul 2020 09:58:49: start X-correlation... INFO @ Tue, 14 Jul 2020 09:58:49: end of X-cor INFO @ Tue, 14 Jul 2020 09:58:49: #2 finished! INFO @ Tue, 14 Jul 2020 09:58:49: #2 predicted fragment length is 231 bps INFO @ Tue, 14 Jul 2020 09:58:49: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 14 Jul 2020 09:58:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.10_model.r WARNING @ Tue, 14 Jul 2020 09:58:49: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:58:49: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Tue, 14 Jul 2020 09:58:49: #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 09:58:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:58:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:58:50: 4000000 INFO @ Tue, 14 Jul 2020 09:58:55: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.10_summits.bed INFO @ Tue, 14 Jul 2020 09:58:58: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1353 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:59:00: 5000000 INFO @ Tue, 14 Jul 2020 09:59:10: 6000000 INFO @ Tue, 14 Jul 2020 09:59:16: #1 tag size is determined as 146 bps INFO @ Tue, 14 Jul 2020 09:59:16: #1 tag size = 146 INFO @ Tue, 14 Jul 2020 09:59:16: #1 total tags in treatment: 2479260 INFO @ Tue, 14 Jul 2020 09:59:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:59:16: #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 09:59:16: #1 tags after filtering in treatment: 2334421 INFO @ Tue, 14 Jul 2020 09:59:16: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 09:59:16: #1 finished! INFO @ Tue, 14 Jul 2020 09:59:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:59:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:59:16: #2 number of paired peaks: 1766 INFO @ Tue, 14 Jul 2020 09:59:16: start model_add_line... INFO @ Tue, 14 Jul 2020 09:59:16: start X-correlation... INFO @ Tue, 14 Jul 2020 09:59:16: end of X-cor INFO @ Tue, 14 Jul 2020 09:59:16: #2 finished! INFO @ Tue, 14 Jul 2020 09:59:16: #2 predicted fragment length is 231 bps INFO @ Tue, 14 Jul 2020 09:59:16: #2 alternative fragment length(s) may be 231 bps INFO @ Tue, 14 Jul 2020 09:59:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.20_model.r WARNING @ Tue, 14 Jul 2020 09:59:16: #2 Since the d (231) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:59:16: #2 You may need to consider one of the other alternative d(s): 231 WARNING @ Tue, 14 Jul 2020 09:59:16: #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 09:59:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:59:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:59:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325352/SRX8325352.20_summits.bed INFO @ Tue, 14 Jul 2020 09:59:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (698 records, 4 fields): 2 millis CompletedMACS2peakCalling