Job ID = 14170590 SRX = SRX8497048 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16583379 spots for SRR11952647/SRR11952647.sra Written 16583379 spots for SRR11952647/SRR11952647.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171068 ("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: 00:24:20 16583379 reads; of these: 16583379 (100.00%) were paired; of these: 1260817 (7.60%) aligned concordantly 0 times 3116968 (18.80%) aligned concordantly exactly 1 time 12205594 (73.60%) aligned concordantly >1 times ---- 1260817 pairs aligned concordantly 0 times; of these: 120155 (9.53%) aligned discordantly 1 time ---- 1140662 pairs aligned 0 times concordantly or discordantly; of these: 2281324 mates make up the pairs; of these: 1221926 (53.56%) aligned 0 times 126217 (5.53%) aligned exactly 1 time 933181 (40.91%) aligned >1 times 96.32% overall alignment rate Time searching: 00:24:20 Overall time: 00:24:20 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] 6845742 / 15401987 = 0.4445 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.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 @ Sat, 11 Dec 2021 07:55:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:55:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:56:03: 1000000 INFO @ Sat, 11 Dec 2021 07:56:09: 2000000 INFO @ Sat, 11 Dec 2021 07:56:16: 3000000 INFO @ Sat, 11 Dec 2021 07:56:22: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:56:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.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 @ Sat, 11 Dec 2021 07:56:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:56:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:56:28: 5000000 INFO @ Sat, 11 Dec 2021 07:56:35: 6000000 INFO @ Sat, 11 Dec 2021 07:56:37: 1000000 INFO @ Sat, 11 Dec 2021 07:56:42: 7000000 INFO @ Sat, 11 Dec 2021 07:56:46: 2000000 INFO @ Sat, 11 Dec 2021 07:56:49: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:56:56: 9000000 INFO @ Sat, 11 Dec 2021 07:56:56: 3000000 INFO @ Sat, 11 Dec 2021 07:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.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 @ Sat, 11 Dec 2021 07:56:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:56:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:57:03: 10000000 INFO @ Sat, 11 Dec 2021 07:57:05: 1000000 INFO @ Sat, 11 Dec 2021 07:57:05: 4000000 INFO @ Sat, 11 Dec 2021 07:57:10: 11000000 INFO @ Sat, 11 Dec 2021 07:57:13: 2000000 INFO @ Sat, 11 Dec 2021 07:57:15: 5000000 INFO @ Sat, 11 Dec 2021 07:57:17: 12000000 INFO @ Sat, 11 Dec 2021 07:57:20: 3000000 INFO @ Sat, 11 Dec 2021 07:57:23: 13000000 INFO @ Sat, 11 Dec 2021 07:57:24: 6000000 INFO @ Sat, 11 Dec 2021 07:57:28: 4000000 INFO @ Sat, 11 Dec 2021 07:57:30: 14000000 INFO @ Sat, 11 Dec 2021 07:57:33: 7000000 INFO @ Sat, 11 Dec 2021 07:57:35: 5000000 INFO @ Sat, 11 Dec 2021 07:57:37: 15000000 INFO @ Sat, 11 Dec 2021 07:57:41: 8000000 INFO @ Sat, 11 Dec 2021 07:57:43: 6000000 INFO @ Sat, 11 Dec 2021 07:57:44: 16000000 INFO @ Sat, 11 Dec 2021 07:57:48: 9000000 INFO @ Sat, 11 Dec 2021 07:57:50: 7000000 INFO @ Sat, 11 Dec 2021 07:57:51: 17000000 INFO @ Sat, 11 Dec 2021 07:57:56: 10000000 INFO @ Sat, 11 Dec 2021 07:57:57: 8000000 INFO @ Sat, 11 Dec 2021 07:57:58: 18000000 INFO @ Sat, 11 Dec 2021 07:58:00: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:58:00: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:58:00: #1 total tags in treatment: 8484792 INFO @ Sat, 11 Dec 2021 07:58:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:58:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:58:00: #1 tags after filtering in treatment: 3898866 INFO @ Sat, 11 Dec 2021 07:58:00: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 11 Dec 2021 07:58:00: #1 finished! INFO @ Sat, 11 Dec 2021 07:58:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:58:00: #2 number of paired peaks: 215 WARNING @ Sat, 11 Dec 2021 07:58:00: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Sat, 11 Dec 2021 07:58:00: start model_add_line... INFO @ Sat, 11 Dec 2021 07:58:00: start X-correlation... INFO @ Sat, 11 Dec 2021 07:58:00: end of X-cor INFO @ Sat, 11 Dec 2021 07:58:00: #2 finished! INFO @ Sat, 11 Dec 2021 07:58:00: #2 predicted fragment length is 143 bps INFO @ Sat, 11 Dec 2021 07:58:00: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 11 Dec 2021 07:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.05_model.r WARNING @ Sat, 11 Dec 2021 07:58:00: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:58:00: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 11 Dec 2021 07:58:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:58:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:58:03: 11000000 INFO @ Sat, 11 Dec 2021 07:58:04: 9000000 INFO @ Sat, 11 Dec 2021 07:58:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:58:10: 12000000 INFO @ Sat, 11 Dec 2021 07:58:11: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:58:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:58:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:58:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.05_summits.bed INFO @ Sat, 11 Dec 2021 07:58:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:58:16: 13000000 INFO @ Sat, 11 Dec 2021 07:58:17: 11000000 INFO @ Sat, 11 Dec 2021 07:58:22: 14000000 INFO @ Sat, 11 Dec 2021 07:58:24: 12000000 INFO @ Sat, 11 Dec 2021 07:58:28: 15000000 INFO @ Sat, 11 Dec 2021 07:58:31: 13000000 INFO @ Sat, 11 Dec 2021 07:58:35: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:58:37: 14000000 INFO @ Sat, 11 Dec 2021 07:58:41: 17000000 INFO @ Sat, 11 Dec 2021 07:58:44: 15000000 INFO @ Sat, 11 Dec 2021 07:58:48: 18000000 INFO @ Sat, 11 Dec 2021 07:58:50: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:58:50: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:58:50: #1 total tags in treatment: 8484792 INFO @ Sat, 11 Dec 2021 07:58:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:58:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:58:50: #1 tags after filtering in treatment: 3898866 INFO @ Sat, 11 Dec 2021 07:58:50: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 11 Dec 2021 07:58:50: #1 finished! INFO @ Sat, 11 Dec 2021 07:58:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:58:50: 16000000 INFO @ Sat, 11 Dec 2021 07:58:50: #2 number of paired peaks: 215 WARNING @ Sat, 11 Dec 2021 07:58:50: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Sat, 11 Dec 2021 07:58:50: start model_add_line... INFO @ Sat, 11 Dec 2021 07:58:50: start X-correlation... INFO @ Sat, 11 Dec 2021 07:58:50: end of X-cor INFO @ Sat, 11 Dec 2021 07:58:50: #2 finished! INFO @ Sat, 11 Dec 2021 07:58:50: #2 predicted fragment length is 143 bps INFO @ Sat, 11 Dec 2021 07:58:50: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 11 Dec 2021 07:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.10_model.r WARNING @ Sat, 11 Dec 2021 07:58:51: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:58:51: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 11 Dec 2021 07:58:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:58:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:58:57: 17000000 INFO @ Sat, 11 Dec 2021 07:58:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:59:03: 18000000 INFO @ Sat, 11 Dec 2021 07:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.10_summits.bed INFO @ Sat, 11 Dec 2021 07:59:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:59:05: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:59:05: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:59:05: #1 total tags in treatment: 8484792 INFO @ Sat, 11 Dec 2021 07:59:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:59:05: #1 tags after filtering in treatment: 3898866 INFO @ Sat, 11 Dec 2021 07:59:05: #1 Redundant rate of treatment: 0.54 INFO @ Sat, 11 Dec 2021 07:59:05: #1 finished! INFO @ Sat, 11 Dec 2021 07:59:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:59:05: #2 number of paired peaks: 215 WARNING @ Sat, 11 Dec 2021 07:59:05: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Sat, 11 Dec 2021 07:59:05: start model_add_line... INFO @ Sat, 11 Dec 2021 07:59:05: start X-correlation... INFO @ Sat, 11 Dec 2021 07:59:05: end of X-cor INFO @ Sat, 11 Dec 2021 07:59:05: #2 finished! INFO @ Sat, 11 Dec 2021 07:59:05: #2 predicted fragment length is 143 bps INFO @ Sat, 11 Dec 2021 07:59:05: #2 alternative fragment length(s) may be 143 bps INFO @ Sat, 11 Dec 2021 07:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.20_model.r WARNING @ Sat, 11 Dec 2021 07:59:06: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:59:06: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sat, 11 Dec 2021 07:59:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:59:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:59:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497048/SRX8497048.20_summits.bed INFO @ Sat, 11 Dec 2021 07:59:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling