Job ID = 6497787 SRX = SRX1389385 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:36:49 prefetch.2.10.7: 1) Downloading 'SRR2834291'... 2020-06-25T22:36:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:38:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:38:58 prefetch.2.10.7: 1) 'SRR2834291' was downloaded successfully Read 16000000 spots for SRR2834291/SRR2834291.sra Written 16000000 spots for SRR2834291/SRR2834291.sra 2020-06-25T22:40:37 prefetch.2.10.7: 1) Downloading 'SRR2834292'... 2020-06-25T22:40:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:41:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:41:53 prefetch.2.10.7: 'SRR2834292' is valid 2020-06-25T22:41:53 prefetch.2.10.7: 1) 'SRR2834292' was downloaded successfully Read 5008132 spots for SRR2834292/SRR2834292.sra Written 5008132 spots for SRR2834292/SRR2834292.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:14:23 21008132 reads; of these: 21008132 (100.00%) were paired; of these: 2231067 (10.62%) aligned concordantly 0 times 7074904 (33.68%) aligned concordantly exactly 1 time 11702161 (55.70%) aligned concordantly >1 times ---- 2231067 pairs aligned concordantly 0 times; of these: 200049 (8.97%) aligned discordantly 1 time ---- 2031018 pairs aligned 0 times concordantly or discordantly; of these: 4062036 mates make up the pairs; of these: 1942324 (47.82%) aligned 0 times 1016188 (25.02%) aligned exactly 1 time 1103524 (27.17%) aligned >1 times 95.38% overall alignment rate Time searching: 01:14:23 Overall time: 01:14:23 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 20 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] 9210222 / 18695578 = 0.4926 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 @ Fri, 26 Jun 2020 09:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.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 @ Fri, 26 Jun 2020 09:06:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:12: 1000000 INFO @ Fri, 26 Jun 2020 09:06:17: 2000000 INFO @ Fri, 26 Jun 2020 09:06:22: 3000000 INFO @ Fri, 26 Jun 2020 09:06:28: 4000000 INFO @ Fri, 26 Jun 2020 09:06:33: 5000000 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 @ Fri, 26 Jun 2020 09:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.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 @ Fri, 26 Jun 2020 09:06:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:38: 6000000 INFO @ Fri, 26 Jun 2020 09:06:43: 1000000 INFO @ Fri, 26 Jun 2020 09:06:44: 7000000 INFO @ Fri, 26 Jun 2020 09:06:48: 2000000 INFO @ Fri, 26 Jun 2020 09:06:50: 8000000 INFO @ Fri, 26 Jun 2020 09:06:54: 3000000 INFO @ Fri, 26 Jun 2020 09:06:56: 9000000 INFO @ Fri, 26 Jun 2020 09:07:00: 4000000 INFO @ Fri, 26 Jun 2020 09:07:01: 10000000 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 @ Fri, 26 Jun 2020 09:07:06: 5000000 INFO @ Fri, 26 Jun 2020 09:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.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 @ Fri, 26 Jun 2020 09:07:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:07:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:07:07: 11000000 INFO @ Fri, 26 Jun 2020 09:07:12: 6000000 INFO @ Fri, 26 Jun 2020 09:07:13: 1000000 INFO @ Fri, 26 Jun 2020 09:07:13: 12000000 INFO @ Fri, 26 Jun 2020 09:07:18: 7000000 INFO @ Fri, 26 Jun 2020 09:07:19: 2000000 INFO @ Fri, 26 Jun 2020 09:07:19: 13000000 INFO @ Fri, 26 Jun 2020 09:07:24: 8000000 INFO @ Fri, 26 Jun 2020 09:07:25: 3000000 INFO @ Fri, 26 Jun 2020 09:07:25: 14000000 INFO @ Fri, 26 Jun 2020 09:07:30: 9000000 INFO @ Fri, 26 Jun 2020 09:07:31: 4000000 INFO @ Fri, 26 Jun 2020 09:07:31: 15000000 INFO @ Fri, 26 Jun 2020 09:07:36: 10000000 INFO @ Fri, 26 Jun 2020 09:07:37: 5000000 INFO @ Fri, 26 Jun 2020 09:07:37: 16000000 INFO @ Fri, 26 Jun 2020 09:07:42: 11000000 INFO @ Fri, 26 Jun 2020 09:07:43: 6000000 INFO @ Fri, 26 Jun 2020 09:07:43: 17000000 INFO @ Fri, 26 Jun 2020 09:07:48: 12000000 INFO @ Fri, 26 Jun 2020 09:07:49: 7000000 INFO @ Fri, 26 Jun 2020 09:07:49: 18000000 INFO @ Fri, 26 Jun 2020 09:07:53: 13000000 INFO @ Fri, 26 Jun 2020 09:07:54: 8000000 INFO @ Fri, 26 Jun 2020 09:07:55: 19000000 INFO @ Fri, 26 Jun 2020 09:07:59: 14000000 INFO @ Fri, 26 Jun 2020 09:08:00: 9000000 INFO @ Fri, 26 Jun 2020 09:08:01: 20000000 INFO @ Fri, 26 Jun 2020 09:08:05: 15000000 INFO @ Fri, 26 Jun 2020 09:08:06: 10000000 INFO @ Fri, 26 Jun 2020 09:08:06: 21000000 INFO @ Fri, 26 Jun 2020 09:08:10: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 09:08:10: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 09:08:10: #1 total tags in treatment: 9570757 INFO @ Fri, 26 Jun 2020 09:08:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:08:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:08:10: #1 tags after filtering in treatment: 7211932 INFO @ Fri, 26 Jun 2020 09:08:10: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 09:08:10: #1 finished! INFO @ Fri, 26 Jun 2020 09:08:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:08:11: 16000000 INFO @ Fri, 26 Jun 2020 09:08:11: #2 number of paired peaks: 916 WARNING @ Fri, 26 Jun 2020 09:08:11: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Fri, 26 Jun 2020 09:08:11: start model_add_line... INFO @ Fri, 26 Jun 2020 09:08:11: start X-correlation... INFO @ Fri, 26 Jun 2020 09:08:11: end of X-cor INFO @ Fri, 26 Jun 2020 09:08:11: #2 finished! INFO @ Fri, 26 Jun 2020 09:08:11: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 09:08:11: #2 alternative fragment length(s) may be 101 bps INFO @ Fri, 26 Jun 2020 09:08:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.05_model.r WARNING @ Fri, 26 Jun 2020 09:08:11: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:08:11: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Fri, 26 Jun 2020 09:08:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:08:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:08:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:08:12: 11000000 INFO @ Fri, 26 Jun 2020 09:08:17: 17000000 INFO @ Fri, 26 Jun 2020 09:08:18: 12000000 INFO @ Fri, 26 Jun 2020 09:08:22: 18000000 INFO @ Fri, 26 Jun 2020 09:08:24: 13000000 INFO @ Fri, 26 Jun 2020 09:08:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:08:28: 19000000 INFO @ Fri, 26 Jun 2020 09:08:29: 14000000 INFO @ Fri, 26 Jun 2020 09:08:34: 20000000 INFO @ Fri, 26 Jun 2020 09:08:35: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:08:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.05_summits.bed INFO @ Fri, 26 Jun 2020 09:08:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2645 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:08:40: 21000000 INFO @ Fri, 26 Jun 2020 09:08:41: 16000000 INFO @ Fri, 26 Jun 2020 09:08:43: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 09:08:43: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 09:08:43: #1 total tags in treatment: 9570757 INFO @ Fri, 26 Jun 2020 09:08:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:08:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:08:44: #1 tags after filtering in treatment: 7211932 INFO @ Fri, 26 Jun 2020 09:08:44: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 09:08:44: #1 finished! INFO @ Fri, 26 Jun 2020 09:08:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:08:44: #2 number of paired peaks: 916 WARNING @ Fri, 26 Jun 2020 09:08:44: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Fri, 26 Jun 2020 09:08:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:08:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:08:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:08:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:08:44: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 09:08:44: #2 alternative fragment length(s) may be 101 bps INFO @ Fri, 26 Jun 2020 09:08:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.10_model.r WARNING @ Fri, 26 Jun 2020 09:08:44: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:08:44: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Fri, 26 Jun 2020 09:08:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:08:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:08:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:08:47: 17000000 INFO @ Fri, 26 Jun 2020 09:08:52: 18000000 INFO @ Fri, 26 Jun 2020 09:08:57: 19000000 INFO @ Fri, 26 Jun 2020 09:09:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:09:03: 20000000 INFO @ Fri, 26 Jun 2020 09:09:08: 21000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.10_summits.bed INFO @ Fri, 26 Jun 2020 09:09:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1460 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:09:11: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 09:09:11: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 09:09:11: #1 total tags in treatment: 9570757 INFO @ Fri, 26 Jun 2020 09:09:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:09:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:09:12: #1 tags after filtering in treatment: 7211932 INFO @ Fri, 26 Jun 2020 09:09:12: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 09:09:12: #1 finished! INFO @ Fri, 26 Jun 2020 09:09:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:09:12: #2 number of paired peaks: 916 WARNING @ Fri, 26 Jun 2020 09:09:12: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Fri, 26 Jun 2020 09:09:12: start model_add_line... INFO @ Fri, 26 Jun 2020 09:09:12: start X-correlation... INFO @ Fri, 26 Jun 2020 09:09:12: end of X-cor INFO @ Fri, 26 Jun 2020 09:09:12: #2 finished! INFO @ Fri, 26 Jun 2020 09:09:12: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 09:09:12: #2 alternative fragment length(s) may be 101 bps INFO @ Fri, 26 Jun 2020 09:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.20_model.r WARNING @ Fri, 26 Jun 2020 09:09:12: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:09:12: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Fri, 26 Jun 2020 09:09:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:09:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:09:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:09:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1389385/SRX1389385.20_summits.bed INFO @ Fri, 26 Jun 2020 09:09:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (890 records, 4 fields): 3 millis CompletedMACS2peakCalling