Job ID = 6627065 SRX = SRX8347280 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:42:23 prefetch.2.10.7: 1) Downloading 'SRR11795463'... 2020-07-14T00:42:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:49:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:49:19 prefetch.2.10.7: 1) 'SRR11795463' was downloaded successfully 2020-07-14T00:49:19 prefetch.2.10.7: 'SRR11795463' has 0 unresolved dependencies Read 13491116 spots for SRR11795463/SRR11795463.sra Written 13491116 spots for SRR11795463/SRR11795463.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627361 ("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: 00:29:30 13491116 reads; of these: 13491116 (100.00%) were paired; of these: 4785973 (35.47%) aligned concordantly 0 times 7140869 (52.93%) aligned concordantly exactly 1 time 1564274 (11.59%) aligned concordantly >1 times ---- 4785973 pairs aligned concordantly 0 times; of these: 681105 (14.23%) aligned discordantly 1 time ---- 4104868 pairs aligned 0 times concordantly or discordantly; of these: 8209736 mates make up the pairs; of these: 7659858 (93.30%) aligned 0 times 216254 (2.63%) aligned exactly 1 time 333624 (4.06%) aligned >1 times 71.61% overall alignment rate Time searching: 00:29:30 Overall time: 00:29:30 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] 3229647 / 9350680 = 0.3454 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 10:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.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 10:27:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:27:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:28:01: 1000000 INFO @ Tue, 14 Jul 2020 10:28:10: 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 10:28:19: 3000000 INFO @ Tue, 14 Jul 2020 10:28:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.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 10:28:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:28:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:28:27: 4000000 INFO @ Tue, 14 Jul 2020 10:28:29: 1000000 INFO @ Tue, 14 Jul 2020 10:28:34: 5000000 INFO @ Tue, 14 Jul 2020 10:28:36: 2000000 INFO @ Tue, 14 Jul 2020 10:28:42: 6000000 INFO @ Tue, 14 Jul 2020 10:28:43: 3000000 INFO @ Tue, 14 Jul 2020 10:28:49: 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 10:28:50: 4000000 INFO @ Tue, 14 Jul 2020 10:28:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.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 10:28:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:28:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:28:56: 8000000 INFO @ Tue, 14 Jul 2020 10:28:58: 5000000 INFO @ Tue, 14 Jul 2020 10:28:59: 1000000 INFO @ Tue, 14 Jul 2020 10:29:03: 9000000 INFO @ Tue, 14 Jul 2020 10:29:05: 6000000 INFO @ Tue, 14 Jul 2020 10:29:07: 2000000 INFO @ Tue, 14 Jul 2020 10:29:09: 10000000 INFO @ Tue, 14 Jul 2020 10:29:12: 7000000 INFO @ Tue, 14 Jul 2020 10:29:16: 3000000 INFO @ Tue, 14 Jul 2020 10:29:16: 11000000 INFO @ Tue, 14 Jul 2020 10:29:20: 8000000 INFO @ Tue, 14 Jul 2020 10:29:22: 12000000 INFO @ Tue, 14 Jul 2020 10:29:24: 4000000 INFO @ Tue, 14 Jul 2020 10:29:28: 9000000 INFO @ Tue, 14 Jul 2020 10:29:28: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:29:28: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:29:28: #1 total tags in treatment: 5625361 INFO @ Tue, 14 Jul 2020 10:29:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:29:28: #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 10:29:28: #1 tags after filtering in treatment: 5499896 INFO @ Tue, 14 Jul 2020 10:29:28: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:29:28: #1 finished! INFO @ Tue, 14 Jul 2020 10:29:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:29:29: #2 number of paired peaks: 132 WARNING @ Tue, 14 Jul 2020 10:29:29: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 14 Jul 2020 10:29:29: start model_add_line... INFO @ Tue, 14 Jul 2020 10:29:29: start X-correlation... INFO @ Tue, 14 Jul 2020 10:29:29: end of X-cor INFO @ Tue, 14 Jul 2020 10:29:29: #2 finished! INFO @ Tue, 14 Jul 2020 10:29:29: #2 predicted fragment length is 186 bps INFO @ Tue, 14 Jul 2020 10:29:29: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 14 Jul 2020 10:29:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.05_model.r WARNING @ Tue, 14 Jul 2020 10:29:29: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:29:29: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Tue, 14 Jul 2020 10:29:29: #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 10:29:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:29:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:29:32: 5000000 INFO @ Tue, 14 Jul 2020 10:29:35: 10000000 INFO @ Tue, 14 Jul 2020 10:29:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:29:40: 6000000 INFO @ Tue, 14 Jul 2020 10:29:42: 11000000 INFO @ Tue, 14 Jul 2020 10:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.05_summits.bed INFO @ Tue, 14 Jul 2020 10:29:46: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (3171 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:29:48: 7000000 INFO @ Tue, 14 Jul 2020 10:29:50: 12000000 INFO @ Tue, 14 Jul 2020 10:29:56: 8000000 INFO @ Tue, 14 Jul 2020 10:29:58: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:29:58: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:29:58: #1 total tags in treatment: 5625361 INFO @ Tue, 14 Jul 2020 10:29:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:29:58: #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 10:29:58: #1 tags after filtering in treatment: 5499896 INFO @ Tue, 14 Jul 2020 10:29:58: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:29:58: #1 finished! INFO @ Tue, 14 Jul 2020 10:29:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:29:58: #2 number of paired peaks: 132 WARNING @ Tue, 14 Jul 2020 10:29:58: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 14 Jul 2020 10:29:58: start model_add_line... INFO @ Tue, 14 Jul 2020 10:29:58: start X-correlation... INFO @ Tue, 14 Jul 2020 10:29:58: end of X-cor INFO @ Tue, 14 Jul 2020 10:29:58: #2 finished! INFO @ Tue, 14 Jul 2020 10:29:58: #2 predicted fragment length is 186 bps INFO @ Tue, 14 Jul 2020 10:29:58: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 14 Jul 2020 10:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.10_model.r WARNING @ Tue, 14 Jul 2020 10:29:58: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:29:58: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Tue, 14 Jul 2020 10:29:58: #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 10:29:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:30:04: 9000000 INFO @ Tue, 14 Jul 2020 10:30:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:30:11: 10000000 INFO @ Tue, 14 Jul 2020 10:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.10_summits.bed INFO @ Tue, 14 Jul 2020 10:30:16: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (798 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:30:19: 11000000 INFO @ Tue, 14 Jul 2020 10:30:27: 12000000 INFO @ Tue, 14 Jul 2020 10:30:34: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:30:34: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:30:34: #1 total tags in treatment: 5625361 INFO @ Tue, 14 Jul 2020 10:30:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:30:34: #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 10:30:34: #1 tags after filtering in treatment: 5499896 INFO @ Tue, 14 Jul 2020 10:30:34: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:30:34: #1 finished! INFO @ Tue, 14 Jul 2020 10:30:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:30:34: #2 number of paired peaks: 132 WARNING @ Tue, 14 Jul 2020 10:30:34: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Tue, 14 Jul 2020 10:30:34: start model_add_line... INFO @ Tue, 14 Jul 2020 10:30:34: start X-correlation... INFO @ Tue, 14 Jul 2020 10:30:34: end of X-cor INFO @ Tue, 14 Jul 2020 10:30:34: #2 finished! INFO @ Tue, 14 Jul 2020 10:30:34: #2 predicted fragment length is 186 bps INFO @ Tue, 14 Jul 2020 10:30:34: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 14 Jul 2020 10:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.20_model.r WARNING @ Tue, 14 Jul 2020 10:30:34: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:30:34: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Tue, 14 Jul 2020 10:30:34: #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 10:30:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:30:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:30:46: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:30:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:30:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:30:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347280/SRX8347280.20_summits.bed INFO @ Tue, 14 Jul 2020 10:30:51: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 1 millis CompletedMACS2peakCalling