Job ID = 16439497 SRX = SRX9518329 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10447286 spots for SRR13070812/SRR13070812.sra Written 10447286 spots for SRR13070812/SRR13070812.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439663 ("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: 00:23:47 10447286 reads; of these: 10447286 (100.00%) were paired; of these: 736073 (7.05%) aligned concordantly 0 times 7201322 (68.93%) aligned concordantly exactly 1 time 2509891 (24.02%) aligned concordantly >1 times ---- 736073 pairs aligned concordantly 0 times; of these: 289211 (39.29%) aligned discordantly 1 time ---- 446862 pairs aligned 0 times concordantly or discordantly; of these: 893724 mates make up the pairs; of these: 496205 (55.52%) aligned 0 times 164584 (18.42%) aligned exactly 1 time 232935 (26.06%) aligned >1 times 97.63% overall alignment rate Time searching: 00:23:47 Overall time: 00:23:47 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 12 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] 193702 / 9957690 = 0.0195 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.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, 02 Aug 2022 15:53:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:25: 1000000 INFO @ Tue, 02 Aug 2022 15:53:32: 2000000 INFO @ Tue, 02 Aug 2022 15:53:40: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:53:47: 4000000 INFO @ Tue, 02 Aug 2022 15:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.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, 02 Aug 2022 15:53:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:53:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:53:54: 1000000 INFO @ Tue, 02 Aug 2022 15:53:55: 5000000 INFO @ Tue, 02 Aug 2022 15:54:01: 2000000 INFO @ Tue, 02 Aug 2022 15:54:03: 6000000 INFO @ Tue, 02 Aug 2022 15:54:09: 3000000 INFO @ Tue, 02 Aug 2022 15:54:10: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:54:16: 4000000 INFO @ Tue, 02 Aug 2022 15:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.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, 02 Aug 2022 15:54:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:54:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:54:18: 8000000 INFO @ Tue, 02 Aug 2022 15:54:23: 5000000 INFO @ Tue, 02 Aug 2022 15:54:24: 1000000 INFO @ Tue, 02 Aug 2022 15:54:26: 9000000 INFO @ Tue, 02 Aug 2022 15:54:31: 6000000 INFO @ Tue, 02 Aug 2022 15:54:32: 2000000 INFO @ Tue, 02 Aug 2022 15:54:34: 10000000 INFO @ Tue, 02 Aug 2022 15:54:38: 7000000 INFO @ Tue, 02 Aug 2022 15:54:39: 3000000 INFO @ Tue, 02 Aug 2022 15:54:41: 11000000 INFO @ Tue, 02 Aug 2022 15:54:46: 8000000 INFO @ Tue, 02 Aug 2022 15:54:46: 4000000 INFO @ Tue, 02 Aug 2022 15:54:49: 12000000 INFO @ Tue, 02 Aug 2022 15:54:54: 5000000 INFO @ Tue, 02 Aug 2022 15:54:54: 9000000 INFO @ Tue, 02 Aug 2022 15:54:57: 13000000 INFO @ Tue, 02 Aug 2022 15:55:01: 6000000 INFO @ Tue, 02 Aug 2022 15:55:02: 10000000 INFO @ Tue, 02 Aug 2022 15:55:04: 14000000 INFO @ Tue, 02 Aug 2022 15:55:09: 7000000 INFO @ Tue, 02 Aug 2022 15:55:10: 11000000 INFO @ Tue, 02 Aug 2022 15:55:12: 15000000 INFO @ Tue, 02 Aug 2022 15:55:17: 8000000 INFO @ Tue, 02 Aug 2022 15:55:18: 12000000 INFO @ Tue, 02 Aug 2022 15:55:20: 16000000 INFO @ Tue, 02 Aug 2022 15:55:25: 9000000 INFO @ Tue, 02 Aug 2022 15:55:26: 13000000 INFO @ Tue, 02 Aug 2022 15:55:28: 17000000 INFO @ Tue, 02 Aug 2022 15:55:33: 10000000 INFO @ Tue, 02 Aug 2022 15:55:34: 14000000 INFO @ Tue, 02 Aug 2022 15:55:36: 18000000 INFO @ Tue, 02 Aug 2022 15:55:41: 11000000 INFO @ Tue, 02 Aug 2022 15:55:41: 15000000 INFO @ Tue, 02 Aug 2022 15:55:44: 19000000 INFO @ Tue, 02 Aug 2022 15:55:49: 16000000 INFO @ Tue, 02 Aug 2022 15:55:49: 12000000 INFO @ Tue, 02 Aug 2022 15:55:51: 20000000 INFO @ Tue, 02 Aug 2022 15:55:52: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:55:52: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:55:52: #1 total tags in treatment: 9520370 INFO @ Tue, 02 Aug 2022 15:55:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:55:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:55:52: #1 tags after filtering in treatment: 9135396 INFO @ Tue, 02 Aug 2022 15:55:52: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:55:52: #1 finished! INFO @ Tue, 02 Aug 2022 15:55:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:55:52: #2 number of paired peaks: 106 WARNING @ Tue, 02 Aug 2022 15:55:52: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 02 Aug 2022 15:55:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:55:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:55:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:55:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:55:52: #2 predicted fragment length is 153 bps INFO @ Tue, 02 Aug 2022 15:55:52: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 02 Aug 2022 15:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.05_model.r WARNING @ Tue, 02 Aug 2022 15:55:53: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:55:53: #2 You may need to consider one of the other alternative d(s): 153 WARNING @ Tue, 02 Aug 2022 15:55:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:55:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:55:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:55:57: 17000000 INFO @ Tue, 02 Aug 2022 15:55:58: 13000000 INFO @ Tue, 02 Aug 2022 15:56:05: 18000000 INFO @ Tue, 02 Aug 2022 15:56:06: 14000000 INFO @ Tue, 02 Aug 2022 15:56:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:13: 19000000 INFO @ Tue, 02 Aug 2022 15:56:14: 15000000 INFO @ Tue, 02 Aug 2022 15:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.05_summits.bed INFO @ Tue, 02 Aug 2022 15:56:20: Done! INFO @ Tue, 02 Aug 2022 15:56:21: 20000000 pass1 - making usageList (13 chroms): 1 millis INFO @ Tue, 02 Aug 2022 15:56:21: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:56:21: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:56:21: #1 total tags in treatment: 9520370 INFO @ Tue, 02 Aug 2022 15:56:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:56:21: #1 tags after filtering in treatment: 9135396 INFO @ Tue, 02 Aug 2022 15:56:21: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:56:21: #1 finished! INFO @ Tue, 02 Aug 2022 15:56:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:56:21: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (965 records, 4 fields): 334 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:56:21: #2 number of paired peaks: 106 WARNING @ Tue, 02 Aug 2022 15:56:21: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 02 Aug 2022 15:56:21: start model_add_line... INFO @ Tue, 02 Aug 2022 15:56:21: start X-correlation... INFO @ Tue, 02 Aug 2022 15:56:21: end of X-cor INFO @ Tue, 02 Aug 2022 15:56:21: #2 finished! INFO @ Tue, 02 Aug 2022 15:56:21: #2 predicted fragment length is 153 bps INFO @ Tue, 02 Aug 2022 15:56:21: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 02 Aug 2022 15:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.10_model.r WARNING @ Tue, 02 Aug 2022 15:56:22: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:56:22: #2 You may need to consider one of the other alternative d(s): 153 WARNING @ Tue, 02 Aug 2022 15:56:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:56:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:56:22: 16000000 INFO @ Tue, 02 Aug 2022 15:56:30: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:56:37: 18000000 INFO @ Tue, 02 Aug 2022 15:56:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:45: 19000000 INFO @ Tue, 02 Aug 2022 15:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.10_summits.bed INFO @ Tue, 02 Aug 2022 15:56:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (500 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:56:53: 20000000 INFO @ Tue, 02 Aug 2022 15:56:53: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:56:53: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:56:53: #1 total tags in treatment: 9520370 INFO @ Tue, 02 Aug 2022 15:56:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:56:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:56:53: #1 tags after filtering in treatment: 9135396 INFO @ Tue, 02 Aug 2022 15:56:53: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:56:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:56:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:56:53: #2 number of paired peaks: 106 WARNING @ Tue, 02 Aug 2022 15:56:53: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 02 Aug 2022 15:56:53: start model_add_line... INFO @ Tue, 02 Aug 2022 15:56:54: start X-correlation... INFO @ Tue, 02 Aug 2022 15:56:54: end of X-cor INFO @ Tue, 02 Aug 2022 15:56:54: #2 finished! INFO @ Tue, 02 Aug 2022 15:56:54: #2 predicted fragment length is 153 bps INFO @ Tue, 02 Aug 2022 15:56:54: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 02 Aug 2022 15:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.20_model.r WARNING @ Tue, 02 Aug 2022 15:56:54: #2 Since the d (153) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:56:54: #2 You may need to consider one of the other alternative d(s): 153 WARNING @ Tue, 02 Aug 2022 15:56:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:56:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:57:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518329/SRX9518329.20_summits.bed INFO @ Tue, 02 Aug 2022 15:57:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 57 millis CompletedMACS2peakCalling