Job ID = 6626973 SRX = SRX7974993 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:07:15 prefetch.2.10.7: 1) Downloading 'SRR11396286'... 2020-07-14T00:07:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:13:58 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:13:58 prefetch.2.10.7: 1) 'SRR11396286' was downloaded successfully Read 12827748 spots for SRR11396286/SRR11396286.sra Written 12827748 spots for SRR11396286/SRR11396286.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627179 ("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: 00:17:55 12827748 reads; of these: 12827748 (100.00%) were paired; of these: 5736191 (44.72%) aligned concordantly 0 times 5738095 (44.73%) aligned concordantly exactly 1 time 1353462 (10.55%) aligned concordantly >1 times ---- 5736191 pairs aligned concordantly 0 times; of these: 195483 (3.41%) aligned discordantly 1 time ---- 5540708 pairs aligned 0 times concordantly or discordantly; of these: 11081416 mates make up the pairs; of these: 10542059 (95.13%) aligned 0 times 291269 (2.63%) aligned exactly 1 time 248088 (2.24%) aligned >1 times 58.91% overall alignment rate Time searching: 00:17:55 Overall time: 00:17:55 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] 2877167 / 7280638 = 0.3952 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 09:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.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 09:38:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:38:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:39:03: 1000000 INFO @ Tue, 14 Jul 2020 09:39:11: 2000000 INFO @ Tue, 14 Jul 2020 09:39:19: 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 09:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.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 09:39:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:39:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:39:27: 4000000 INFO @ Tue, 14 Jul 2020 09:39:33: 1000000 INFO @ Tue, 14 Jul 2020 09:39:36: 5000000 INFO @ Tue, 14 Jul 2020 09:39:41: 2000000 INFO @ Tue, 14 Jul 2020 09:39:44: 6000000 INFO @ Tue, 14 Jul 2020 09:39:49: 3000000 INFO @ Tue, 14 Jul 2020 09:39:53: 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 09:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.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 09:39:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:39:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:39:56: 4000000 INFO @ Tue, 14 Jul 2020 09:40:01: 8000000 INFO @ Tue, 14 Jul 2020 09:40:04: 1000000 INFO @ Tue, 14 Jul 2020 09:40:04: 5000000 INFO @ Tue, 14 Jul 2020 09:40:10: 9000000 INFO @ Tue, 14 Jul 2020 09:40:13: 6000000 INFO @ Tue, 14 Jul 2020 09:40:13: 2000000 INFO @ Tue, 14 Jul 2020 09:40:13: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 09:40:13: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 09:40:13: #1 total tags in treatment: 4258006 INFO @ Tue, 14 Jul 2020 09:40:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:40:13: #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 09:40:13: #1 tags after filtering in treatment: 4157473 INFO @ Tue, 14 Jul 2020 09:40:13: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 09:40:13: #1 finished! INFO @ Tue, 14 Jul 2020 09:40:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:40:13: #2 number of paired peaks: 226 WARNING @ Tue, 14 Jul 2020 09:40:13: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 14 Jul 2020 09:40:13: start model_add_line... INFO @ Tue, 14 Jul 2020 09:40:13: start X-correlation... INFO @ Tue, 14 Jul 2020 09:40:13: end of X-cor INFO @ Tue, 14 Jul 2020 09:40:13: #2 finished! INFO @ Tue, 14 Jul 2020 09:40:13: #2 predicted fragment length is 145 bps INFO @ Tue, 14 Jul 2020 09:40:13: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 14 Jul 2020 09:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.05_model.r WARNING @ Tue, 14 Jul 2020 09:40:13: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:40:13: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Tue, 14 Jul 2020 09:40:13: #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 09:40:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:40:21: 7000000 INFO @ Tue, 14 Jul 2020 09:40:22: 3000000 INFO @ Tue, 14 Jul 2020 09:40:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:40:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:40:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:40:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.05_summits.bed INFO @ Tue, 14 Jul 2020 09:40:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1320 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:40:28: 8000000 INFO @ Tue, 14 Jul 2020 09:40:30: 4000000 INFO @ Tue, 14 Jul 2020 09:40:36: 9000000 INFO @ Tue, 14 Jul 2020 09:40:39: 5000000 INFO @ Tue, 14 Jul 2020 09:40:39: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 09:40:39: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 09:40:39: #1 total tags in treatment: 4258006 INFO @ Tue, 14 Jul 2020 09:40:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:40:39: #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 09:40:39: #1 tags after filtering in treatment: 4157473 INFO @ Tue, 14 Jul 2020 09:40:39: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 09:40:39: #1 finished! INFO @ Tue, 14 Jul 2020 09:40:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:40:39: #2 number of paired peaks: 226 WARNING @ Tue, 14 Jul 2020 09:40:39: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 14 Jul 2020 09:40:39: start model_add_line... INFO @ Tue, 14 Jul 2020 09:40:39: start X-correlation... INFO @ Tue, 14 Jul 2020 09:40:39: end of X-cor INFO @ Tue, 14 Jul 2020 09:40:39: #2 finished! INFO @ Tue, 14 Jul 2020 09:40:39: #2 predicted fragment length is 145 bps INFO @ Tue, 14 Jul 2020 09:40:39: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 14 Jul 2020 09:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.10_model.r WARNING @ Tue, 14 Jul 2020 09:40:39: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:40:39: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Tue, 14 Jul 2020 09:40:39: #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 09:40:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:40:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:40:47: 6000000 INFO @ Tue, 14 Jul 2020 09:40:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:40:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:40:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:40:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.10_summits.bed INFO @ Tue, 14 Jul 2020 09:40:52: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (495 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:40:55: 7000000 INFO @ Tue, 14 Jul 2020 09:41:03: 8000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:41:11: 9000000 INFO @ Tue, 14 Jul 2020 09:41:14: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 09:41:14: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 09:41:14: #1 total tags in treatment: 4258006 INFO @ Tue, 14 Jul 2020 09:41:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:41:14: #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 09:41:14: #1 tags after filtering in treatment: 4157473 INFO @ Tue, 14 Jul 2020 09:41:14: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 09:41:14: #1 finished! INFO @ Tue, 14 Jul 2020 09:41:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:41:14: #2 number of paired peaks: 226 WARNING @ Tue, 14 Jul 2020 09:41:14: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 14 Jul 2020 09:41:14: start model_add_line... INFO @ Tue, 14 Jul 2020 09:41:14: start X-correlation... INFO @ Tue, 14 Jul 2020 09:41:14: end of X-cor INFO @ Tue, 14 Jul 2020 09:41:14: #2 finished! INFO @ Tue, 14 Jul 2020 09:41:14: #2 predicted fragment length is 145 bps INFO @ Tue, 14 Jul 2020 09:41:14: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 14 Jul 2020 09:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.20_model.r WARNING @ Tue, 14 Jul 2020 09:41:14: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:41:14: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Tue, 14 Jul 2020 09:41:14: #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 09:41:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:41:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:41:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974993/SRX7974993.20_summits.bed INFO @ Tue, 14 Jul 2020 09:41:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling