Job ID = 6627063 SRX = SRX8347278 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:41:50 prefetch.2.10.7: 1) Downloading 'SRR11795461'... 2020-07-14T00:41:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:48:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:48:44 prefetch.2.10.7: 1) 'SRR11795461' was downloaded successfully 2020-07-14T00:48:44 prefetch.2.10.7: 'SRR11795461' has 0 unresolved dependencies Read 14815907 spots for SRR11795461/SRR11795461.sra Written 14815907 spots for SRR11795461/SRR11795461.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627400 ("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: 00:41:00 14815907 reads; of these: 14815907 (100.00%) were paired; of these: 5552774 (37.48%) aligned concordantly 0 times 7380150 (49.81%) aligned concordantly exactly 1 time 1882983 (12.71%) aligned concordantly >1 times ---- 5552774 pairs aligned concordantly 0 times; of these: 764034 (13.76%) aligned discordantly 1 time ---- 4788740 pairs aligned 0 times concordantly or discordantly; of these: 9577480 mates make up the pairs; of these: 8809717 (91.98%) aligned 0 times 305197 (3.19%) aligned exactly 1 time 462566 (4.83%) aligned >1 times 70.27% overall alignment rate Time searching: 00:41:00 Overall time: 00:41:00 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] 5530217 / 9991417 = 0.5535 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 10:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.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 10:39:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:39:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:39:28: 1000000 INFO @ Tue, 14 Jul 2020 10:39:36: 2000000 INFO @ Tue, 14 Jul 2020 10:39:44: 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 10:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.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 10:39:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:39:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:39:52: 4000000 INFO @ Tue, 14 Jul 2020 10:40:00: 5000000 INFO @ Tue, 14 Jul 2020 10:40:02: 1000000 INFO @ Tue, 14 Jul 2020 10:40:08: 6000000 INFO @ Tue, 14 Jul 2020 10:40:13: 2000000 INFO @ Tue, 14 Jul 2020 10:40:16: 7000000 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 10:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.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 10:40:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:40:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:40:24: 3000000 INFO @ Tue, 14 Jul 2020 10:40:25: 8000000 INFO @ Tue, 14 Jul 2020 10:40:29: 1000000 INFO @ Tue, 14 Jul 2020 10:40:33: 9000000 INFO @ Tue, 14 Jul 2020 10:40:35: 4000000 INFO @ Tue, 14 Jul 2020 10:40:38: 2000000 INFO @ Tue, 14 Jul 2020 10:40:39: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:40:39: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:40:39: #1 total tags in treatment: 4024097 INFO @ Tue, 14 Jul 2020 10:40:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:40:39: #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 10:40:39: #1 tags after filtering in treatment: 3861093 INFO @ Tue, 14 Jul 2020 10:40:39: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:40:39: #1 finished! INFO @ Tue, 14 Jul 2020 10:40:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:40:40: #2 number of paired peaks: 2305 INFO @ Tue, 14 Jul 2020 10:40:40: start model_add_line... INFO @ Tue, 14 Jul 2020 10:40:40: start X-correlation... INFO @ Tue, 14 Jul 2020 10:40:40: end of X-cor INFO @ Tue, 14 Jul 2020 10:40:40: #2 finished! INFO @ Tue, 14 Jul 2020 10:40:40: #2 predicted fragment length is 240 bps INFO @ Tue, 14 Jul 2020 10:40:40: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 14 Jul 2020 10:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.05_model.r WARNING @ Tue, 14 Jul 2020 10:40:40: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:40:40: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 14 Jul 2020 10:40:40: #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 10:40:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:40:45: 5000000 INFO @ Tue, 14 Jul 2020 10:40:47: 3000000 INFO @ Tue, 14 Jul 2020 10:40:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.05_summits.bed INFO @ Tue, 14 Jul 2020 10:40:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5340 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:40:55: 6000000 INFO @ Tue, 14 Jul 2020 10:40:56: 4000000 INFO @ Tue, 14 Jul 2020 10:41:04: 5000000 INFO @ Tue, 14 Jul 2020 10:41:05: 7000000 INFO @ Tue, 14 Jul 2020 10:41:12: 6000000 INFO @ Tue, 14 Jul 2020 10:41:15: 8000000 INFO @ Tue, 14 Jul 2020 10:41:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:41:25: 9000000 INFO @ Tue, 14 Jul 2020 10:41:29: 8000000 INFO @ Tue, 14 Jul 2020 10:41:33: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:41:33: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:41:33: #1 total tags in treatment: 4024097 INFO @ Tue, 14 Jul 2020 10:41:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:41:33: #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 10:41:33: #1 tags after filtering in treatment: 3861093 INFO @ Tue, 14 Jul 2020 10:41:33: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:41:33: #1 finished! INFO @ Tue, 14 Jul 2020 10:41:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:41:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:41:34: #2 number of paired peaks: 2305 INFO @ Tue, 14 Jul 2020 10:41:34: start model_add_line... INFO @ Tue, 14 Jul 2020 10:41:34: start X-correlation... INFO @ Tue, 14 Jul 2020 10:41:34: end of X-cor INFO @ Tue, 14 Jul 2020 10:41:34: #2 finished! INFO @ Tue, 14 Jul 2020 10:41:34: #2 predicted fragment length is 240 bps INFO @ Tue, 14 Jul 2020 10:41:34: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 14 Jul 2020 10:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.10_model.r WARNING @ Tue, 14 Jul 2020 10:41:34: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:41:34: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 14 Jul 2020 10:41:34: #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 10:41:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:41:38: 9000000 INFO @ Tue, 14 Jul 2020 10:41:44: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:41:44: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:41:44: #1 total tags in treatment: 4024097 INFO @ Tue, 14 Jul 2020 10:41:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:41:44: #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 10:41:44: #1 tags after filtering in treatment: 3861093 INFO @ Tue, 14 Jul 2020 10:41:44: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:41:44: #1 finished! INFO @ Tue, 14 Jul 2020 10:41:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:41:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:41:44: #2 number of paired peaks: 2305 INFO @ Tue, 14 Jul 2020 10:41:44: start model_add_line... INFO @ Tue, 14 Jul 2020 10:41:44: start X-correlation... INFO @ Tue, 14 Jul 2020 10:41:44: end of X-cor INFO @ Tue, 14 Jul 2020 10:41:44: #2 finished! INFO @ Tue, 14 Jul 2020 10:41:44: #2 predicted fragment length is 240 bps INFO @ Tue, 14 Jul 2020 10:41:44: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 14 Jul 2020 10:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.20_model.r WARNING @ Tue, 14 Jul 2020 10:41:44: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:41:44: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 14 Jul 2020 10:41:44: #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 10:41:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:41:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:41:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:41:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:41:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.10_summits.bed INFO @ Tue, 14 Jul 2020 10:41:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3349 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:41:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347278/SRX8347278.20_summits.bed INFO @ Tue, 14 Jul 2020 10:41:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1735 records, 4 fields): 4 millis CompletedMACS2peakCalling