Job ID = 14167424 SRX = ERX3978909 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27057490 spots for ERR3975978/ERR3975978.sra Written 27057490 spots for ERR3975978/ERR3975978.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168525 ("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: 01:50:40 27057490 reads; of these: 27057490 (100.00%) were paired; of these: 2999136 (11.08%) aligned concordantly 0 times 18482544 (68.31%) aligned concordantly exactly 1 time 5575810 (20.61%) aligned concordantly >1 times ---- 2999136 pairs aligned concordantly 0 times; of these: 493409 (16.45%) aligned discordantly 1 time ---- 2505727 pairs aligned 0 times concordantly or discordantly; of these: 5011454 mates make up the pairs; of these: 2463251 (49.15%) aligned 0 times 1308375 (26.11%) aligned exactly 1 time 1239828 (24.74%) aligned >1 times 95.45% overall alignment rate Time searching: 01:50:40 Overall time: 01:50:40 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 24 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] 16230082 / 24437272 = 0.6642 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 @ Fri, 10 Dec 2021 14:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.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, 10 Dec 2021 14:26:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:26:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:26:52: 1000000 INFO @ Fri, 10 Dec 2021 14:26:58: 2000000 INFO @ Fri, 10 Dec 2021 14:27:03: 3000000 INFO @ Fri, 10 Dec 2021 14:27:09: 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 @ Fri, 10 Dec 2021 14:27:14: 5000000 INFO @ Fri, 10 Dec 2021 14:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.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, 10 Dec 2021 14:27:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:27:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:27:20: 6000000 INFO @ Fri, 10 Dec 2021 14:27:23: 1000000 INFO @ Fri, 10 Dec 2021 14:27:26: 7000000 INFO @ Fri, 10 Dec 2021 14:27:29: 2000000 INFO @ Fri, 10 Dec 2021 14:27:32: 8000000 INFO @ Fri, 10 Dec 2021 14:27:35: 3000000 INFO @ Fri, 10 Dec 2021 14:27:38: 9000000 INFO @ Fri, 10 Dec 2021 14:27:42: 4000000 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 @ Fri, 10 Dec 2021 14:27:44: 10000000 INFO @ Fri, 10 Dec 2021 14:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.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, 10 Dec 2021 14:27:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:27:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:27:48: 5000000 INFO @ Fri, 10 Dec 2021 14:27:51: 11000000 INFO @ Fri, 10 Dec 2021 14:27:53: 1000000 INFO @ Fri, 10 Dec 2021 14:27:54: 6000000 INFO @ Fri, 10 Dec 2021 14:27:57: 12000000 INFO @ Fri, 10 Dec 2021 14:27:59: 2000000 INFO @ Fri, 10 Dec 2021 14:28:00: 7000000 INFO @ Fri, 10 Dec 2021 14:28:04: 13000000 INFO @ Fri, 10 Dec 2021 14:28:05: 3000000 INFO @ Fri, 10 Dec 2021 14:28:07: 8000000 INFO @ Fri, 10 Dec 2021 14:28:11: 14000000 INFO @ Fri, 10 Dec 2021 14:28:11: 4000000 INFO @ Fri, 10 Dec 2021 14:28:13: 9000000 INFO @ Fri, 10 Dec 2021 14:28:17: 5000000 INFO @ Fri, 10 Dec 2021 14:28:17: 15000000 INFO @ Fri, 10 Dec 2021 14:28:19: 10000000 INFO @ Fri, 10 Dec 2021 14:28:23: 6000000 INFO @ Fri, 10 Dec 2021 14:28:24: 16000000 INFO @ Fri, 10 Dec 2021 14:28:26: 11000000 INFO @ Fri, 10 Dec 2021 14:28:29: 7000000 INFO @ Fri, 10 Dec 2021 14:28:30: 17000000 INFO @ Fri, 10 Dec 2021 14:28:32: 12000000 INFO @ Fri, 10 Dec 2021 14:28:35: 8000000 INFO @ Fri, 10 Dec 2021 14:28:37: 18000000 INFO @ Fri, 10 Dec 2021 14:28:38: 13000000 INFO @ Fri, 10 Dec 2021 14:28:41: 9000000 INFO @ Fri, 10 Dec 2021 14:28:44: 19000000 INFO @ Fri, 10 Dec 2021 14:28:45: 14000000 INFO @ Fri, 10 Dec 2021 14:28:45: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 14:28:45: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 14:28:45: #1 total tags in treatment: 8145900 INFO @ Fri, 10 Dec 2021 14:28:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:28:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:28:45: #1 tags after filtering in treatment: 7534947 INFO @ Fri, 10 Dec 2021 14:28:45: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 14:28:45: #1 finished! INFO @ Fri, 10 Dec 2021 14:28:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:28:46: #2 number of paired peaks: 911 WARNING @ Fri, 10 Dec 2021 14:28:46: Fewer paired peaks (911) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 911 pairs to build model! INFO @ Fri, 10 Dec 2021 14:28:46: start model_add_line... INFO @ Fri, 10 Dec 2021 14:28:46: start X-correlation... INFO @ Fri, 10 Dec 2021 14:28:46: end of X-cor INFO @ Fri, 10 Dec 2021 14:28:46: #2 finished! INFO @ Fri, 10 Dec 2021 14:28:46: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 14:28:46: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 14:28:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.05_model.r WARNING @ Fri, 10 Dec 2021 14:28:46: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:28:46: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 14:28:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:28:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:28:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:28:47: 10000000 INFO @ Fri, 10 Dec 2021 14:28:51: 15000000 INFO @ Fri, 10 Dec 2021 14:28:53: 11000000 INFO @ Fri, 10 Dec 2021 14:28:57: 16000000 INFO @ Fri, 10 Dec 2021 14:28:59: 12000000 INFO @ Fri, 10 Dec 2021 14:29:03: 17000000 INFO @ Fri, 10 Dec 2021 14:29:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:29:05: 13000000 INFO @ Fri, 10 Dec 2021 14:29:09: 18000000 INFO @ Fri, 10 Dec 2021 14:29:10: 14000000 INFO @ Fri, 10 Dec 2021 14:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.05_summits.bed INFO @ Fri, 10 Dec 2021 14:29:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6108 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:29:14: 19000000 INFO @ Fri, 10 Dec 2021 14:29:15: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 14:29:15: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 14:29:15: #1 total tags in treatment: 8145900 INFO @ Fri, 10 Dec 2021 14:29:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:29:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:29:15: #1 tags after filtering in treatment: 7534947 INFO @ Fri, 10 Dec 2021 14:29:15: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 14:29:15: #1 finished! INFO @ Fri, 10 Dec 2021 14:29:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:29:16: #2 number of paired peaks: 911 WARNING @ Fri, 10 Dec 2021 14:29:16: Fewer paired peaks (911) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 911 pairs to build model! INFO @ Fri, 10 Dec 2021 14:29:16: start model_add_line... INFO @ Fri, 10 Dec 2021 14:29:16: start X-correlation... INFO @ Fri, 10 Dec 2021 14:29:16: end of X-cor INFO @ Fri, 10 Dec 2021 14:29:16: #2 finished! INFO @ Fri, 10 Dec 2021 14:29:16: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 14:29:16: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 14:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.10_model.r WARNING @ Fri, 10 Dec 2021 14:29:16: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:29:16: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 14:29:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:29:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:29:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:29:16: 15000000 INFO @ Fri, 10 Dec 2021 14:29:22: 16000000 INFO @ Fri, 10 Dec 2021 14:29:28: 17000000 INFO @ Fri, 10 Dec 2021 14:29:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:29:34: 18000000 INFO @ Fri, 10 Dec 2021 14:29:40: 19000000 INFO @ Fri, 10 Dec 2021 14:29:41: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 14:29:41: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 14:29:41: #1 total tags in treatment: 8145900 INFO @ Fri, 10 Dec 2021 14:29:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:29:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:29:41: #1 tags after filtering in treatment: 7534947 INFO @ Fri, 10 Dec 2021 14:29:41: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 14:29:41: #1 finished! INFO @ Fri, 10 Dec 2021 14:29:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:29:42: #2 number of paired peaks: 911 WARNING @ Fri, 10 Dec 2021 14:29:42: Fewer paired peaks (911) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 911 pairs to build model! INFO @ Fri, 10 Dec 2021 14:29:42: start model_add_line... INFO @ Fri, 10 Dec 2021 14:29:42: start X-correlation... INFO @ Fri, 10 Dec 2021 14:29:42: end of X-cor INFO @ Fri, 10 Dec 2021 14:29:42: #2 finished! INFO @ Fri, 10 Dec 2021 14:29:42: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 14:29:42: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 14:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.20_model.r WARNING @ Fri, 10 Dec 2021 14:29:42: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:29:42: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 14:29:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:29:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.10_summits.bed INFO @ Fri, 10 Dec 2021 14:29:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2444 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:29:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978909/ERX3978909.20_summits.bed INFO @ Fri, 10 Dec 2021 14:30:09: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1064 records, 4 fields): 32 millis CompletedMACS2peakCalling BigWig に変換しました。