Job ID = 14168519 SRX = ERX3978752 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13979983 spots for ERR3975764/ERR3975764.sra Written 13979983 spots for ERR3975764/ERR3975764.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169678 ("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: 00:25:16 13979983 reads; of these: 13979983 (100.00%) were paired; of these: 6152593 (44.01%) aligned concordantly 0 times 2952101 (21.12%) aligned concordantly exactly 1 time 4875289 (34.87%) aligned concordantly >1 times ---- 6152593 pairs aligned concordantly 0 times; of these: 795038 (12.92%) aligned discordantly 1 time ---- 5357555 pairs aligned 0 times concordantly or discordantly; of these: 10715110 mates make up the pairs; of these: 6980661 (65.15%) aligned 0 times 217961 (2.03%) aligned exactly 1 time 3516488 (32.82%) aligned >1 times 75.03% overall alignment rate Time searching: 00:25:16 Overall time: 00:25:16 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] 3581451 / 8542349 = 0.4193 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 19:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.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 19:18:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:18:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:09: 1000000 INFO @ Fri, 10 Dec 2021 19:18:18: 2000000 INFO @ Fri, 10 Dec 2021 19:18:26: 3000000 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 19:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.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 19:18:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:18:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:18:35: 4000000 INFO @ Fri, 10 Dec 2021 19:18:38: 1000000 INFO @ Fri, 10 Dec 2021 19:18:44: 5000000 INFO @ Fri, 10 Dec 2021 19:18:46: 2000000 INFO @ Fri, 10 Dec 2021 19:18:53: 6000000 INFO @ Fri, 10 Dec 2021 19:18:54: 3000000 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 19:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.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 19:19:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:19:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:19:02: 4000000 INFO @ Fri, 10 Dec 2021 19:19:02: 7000000 INFO @ Fri, 10 Dec 2021 19:19:10: 5000000 INFO @ Fri, 10 Dec 2021 19:19:10: 1000000 INFO @ Fri, 10 Dec 2021 19:19:11: 8000000 INFO @ Fri, 10 Dec 2021 19:19:17: 6000000 INFO @ Fri, 10 Dec 2021 19:19:19: 2000000 INFO @ Fri, 10 Dec 2021 19:19:20: 9000000 INFO @ Fri, 10 Dec 2021 19:19:25: 7000000 INFO @ Fri, 10 Dec 2021 19:19:28: 3000000 INFO @ Fri, 10 Dec 2021 19:19:29: 10000000 INFO @ Fri, 10 Dec 2021 19:19:32: 8000000 INFO @ Fri, 10 Dec 2021 19:19:37: 11000000 INFO @ Fri, 10 Dec 2021 19:19:37: 4000000 INFO @ Fri, 10 Dec 2021 19:19:39: 9000000 INFO @ Fri, 10 Dec 2021 19:19:46: 12000000 INFO @ Fri, 10 Dec 2021 19:19:46: 5000000 INFO @ Fri, 10 Dec 2021 19:19:47: 10000000 INFO @ Fri, 10 Dec 2021 19:19:54: 11000000 INFO @ Fri, 10 Dec 2021 19:19:55: 13000000 INFO @ Fri, 10 Dec 2021 19:19:56: 6000000 INFO @ Fri, 10 Dec 2021 19:20:02: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:20:03: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:20:03: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:20:03: #1 total tags in treatment: 4313968 INFO @ Fri, 10 Dec 2021 19:20:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:20:03: #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 19:20:03: #1 tags after filtering in treatment: 3052735 INFO @ Fri, 10 Dec 2021 19:20:03: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:20:03: #1 finished! INFO @ Fri, 10 Dec 2021 19:20:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:20:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:20:03: #2 number of paired peaks: 4831 INFO @ Fri, 10 Dec 2021 19:20:03: start model_add_line... INFO @ Fri, 10 Dec 2021 19:20:03: start X-correlation... INFO @ Fri, 10 Dec 2021 19:20:03: end of X-cor INFO @ Fri, 10 Dec 2021 19:20:03: #2 finished! INFO @ Fri, 10 Dec 2021 19:20:03: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 19:20:03: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 19:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.05_model.r WARNING @ Fri, 10 Dec 2021 19:20:03: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:20:03: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 19:20:03: #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 19:20:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:20:04: 7000000 INFO @ Fri, 10 Dec 2021 19:20:10: 13000000 INFO @ Fri, 10 Dec 2021 19:20:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:20:13: 8000000 INFO @ Fri, 10 Dec 2021 19:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.05_summits.bed INFO @ Fri, 10 Dec 2021 19:20:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7938 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:20:16: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:20:16: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:20:16: #1 total tags in treatment: 4313968 INFO @ Fri, 10 Dec 2021 19:20:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:20:16: #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 19:20:16: #1 tags after filtering in treatment: 3052735 INFO @ Fri, 10 Dec 2021 19:20:16: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:20:16: #1 finished! INFO @ Fri, 10 Dec 2021 19:20:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:20:16: #2 number of paired peaks: 4831 INFO @ Fri, 10 Dec 2021 19:20:17: start model_add_line... INFO @ Fri, 10 Dec 2021 19:20:17: start X-correlation... INFO @ Fri, 10 Dec 2021 19:20:17: end of X-cor INFO @ Fri, 10 Dec 2021 19:20:17: #2 finished! INFO @ Fri, 10 Dec 2021 19:20:17: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 19:20:17: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 19:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.10_model.r WARNING @ Fri, 10 Dec 2021 19:20:17: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:20:17: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 19:20:17: #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 19:20:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:20:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:20:21: 9000000 INFO @ Fri, 10 Dec 2021 19:20:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.10_summits.bed INFO @ Fri, 10 Dec 2021 19:20:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4114 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:20:29: 10000000 INFO @ Fri, 10 Dec 2021 19:20:37: 11000000 INFO @ Fri, 10 Dec 2021 19:20:45: 12000000 INFO @ Fri, 10 Dec 2021 19:20:54: 13000000 INFO @ Fri, 10 Dec 2021 19:21:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:21:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:21:01: #1 total tags in treatment: 4313968 INFO @ Fri, 10 Dec 2021 19:21:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:21:01: #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 19:21:01: #1 tags after filtering in treatment: 3052735 INFO @ Fri, 10 Dec 2021 19:21:01: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:21:01: #1 finished! INFO @ Fri, 10 Dec 2021 19:21:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:21:01: #2 number of paired peaks: 4831 INFO @ Fri, 10 Dec 2021 19:21:01: start model_add_line... INFO @ Fri, 10 Dec 2021 19:21:01: start X-correlation... INFO @ Fri, 10 Dec 2021 19:21:01: end of X-cor INFO @ Fri, 10 Dec 2021 19:21:01: #2 finished! INFO @ Fri, 10 Dec 2021 19:21:01: #2 predicted fragment length is 203 bps INFO @ Fri, 10 Dec 2021 19:21:01: #2 alternative fragment length(s) may be 203 bps INFO @ Fri, 10 Dec 2021 19:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.20_model.r WARNING @ Fri, 10 Dec 2021 19:21:01: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:21:01: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Fri, 10 Dec 2021 19:21:01: #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 19:21:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:21:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978752/ERX3978752.20_summits.bed INFO @ Fri, 10 Dec 2021 19:21:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1395 records, 4 fields): 3 millis CompletedMACS2peakCalling