Job ID = 14168269 SRX = ERX3978845 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19668192 spots for ERR3975914/ERR3975914.sra Written 19668192 spots for ERR3975914/ERR3975914.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169651 ("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: 02:12:44 19668192 reads; of these: 19668192 (100.00%) were paired; of these: 7006913 (35.63%) aligned concordantly 0 times 9455396 (48.07%) aligned concordantly exactly 1 time 3205883 (16.30%) aligned concordantly >1 times ---- 7006913 pairs aligned concordantly 0 times; of these: 545932 (7.79%) aligned discordantly 1 time ---- 6460981 pairs aligned 0 times concordantly or discordantly; of these: 12921962 mates make up the pairs; of these: 6031024 (46.67%) aligned 0 times 3933488 (30.44%) aligned exactly 1 time 2957450 (22.89%) aligned >1 times 84.67% overall alignment rate Time searching: 02:12:44 Overall time: 02:12:44 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] 10569593 / 13042689 = 0.8104 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 19:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.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 19:10:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:10:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:10:44: 1000000 INFO @ Fri, 10 Dec 2021 19:10:53: 2000000 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 19:11:01: 3000000 INFO @ Fri, 10 Dec 2021 19:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.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 19:11:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:11:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:11:10: 4000000 INFO @ Fri, 10 Dec 2021 19:11:11: 1000000 INFO @ Fri, 10 Dec 2021 19:11:18: 5000000 INFO @ Fri, 10 Dec 2021 19:11:20: 2000000 INFO @ Fri, 10 Dec 2021 19:11:26: 6000000 INFO @ Fri, 10 Dec 2021 19:11:28: 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 19:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.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 19:11:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:11:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:11:35: 7000000 INFO @ Fri, 10 Dec 2021 19:11:37: 4000000 INFO @ Fri, 10 Dec 2021 19:11:43: 1000000 INFO @ Fri, 10 Dec 2021 19:11:44: 8000000 INFO @ Fri, 10 Dec 2021 19:11:45: 5000000 INFO @ Fri, 10 Dec 2021 19:11:52: 2000000 INFO @ Fri, 10 Dec 2021 19:11:53: 9000000 INFO @ Fri, 10 Dec 2021 19:11:54: 6000000 INFO @ Fri, 10 Dec 2021 19:12:00: 3000000 INFO @ Fri, 10 Dec 2021 19:12:02: 7000000 INFO @ Fri, 10 Dec 2021 19:12:02: 10000000 INFO @ Fri, 10 Dec 2021 19:12:08: 4000000 INFO @ Fri, 10 Dec 2021 19:12:11: 8000000 INFO @ Fri, 10 Dec 2021 19:12:11: 11000000 INFO @ Fri, 10 Dec 2021 19:12:16: 5000000 INFO @ Fri, 10 Dec 2021 19:12:20: 12000000 INFO @ Fri, 10 Dec 2021 19:12:20: 9000000 INFO @ Fri, 10 Dec 2021 19:12:21: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:12:21: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:12:21: #1 total tags in treatment: 2466533 INFO @ Fri, 10 Dec 2021 19:12:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:12:21: #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 19:12:21: #1 tags after filtering in treatment: 2100763 INFO @ Fri, 10 Dec 2021 19:12:21: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:12:21: #1 finished! INFO @ Fri, 10 Dec 2021 19:12:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:12:21: #2 number of paired peaks: 4748 INFO @ Fri, 10 Dec 2021 19:12:21: start model_add_line... INFO @ Fri, 10 Dec 2021 19:12:21: start X-correlation... INFO @ Fri, 10 Dec 2021 19:12:22: end of X-cor INFO @ Fri, 10 Dec 2021 19:12:22: #2 finished! INFO @ Fri, 10 Dec 2021 19:12:22: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 19:12:22: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 19:12:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.05_model.r WARNING @ Fri, 10 Dec 2021 19:12:22: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:12:22: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 19:12:22: #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 19:12:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:12:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:12:24: 6000000 INFO @ Fri, 10 Dec 2021 19:12:28: 10000000 INFO @ Fri, 10 Dec 2021 19:12:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.05_summits.bed INFO @ Fri, 10 Dec 2021 19:12:33: Done! INFO @ Fri, 10 Dec 2021 19:12:33: 7000000 pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7020 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:12:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:12:42: 8000000 INFO @ Fri, 10 Dec 2021 19:12:43: 12000000 INFO @ Fri, 10 Dec 2021 19:12:44: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:12:44: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:12:44: #1 total tags in treatment: 2466533 INFO @ Fri, 10 Dec 2021 19:12:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:12:44: #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 19:12:44: #1 tags after filtering in treatment: 2100763 INFO @ Fri, 10 Dec 2021 19:12:44: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:12:44: #1 finished! INFO @ Fri, 10 Dec 2021 19:12:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:12:45: #2 number of paired peaks: 4748 INFO @ Fri, 10 Dec 2021 19:12:45: start model_add_line... INFO @ Fri, 10 Dec 2021 19:12:45: start X-correlation... INFO @ Fri, 10 Dec 2021 19:12:45: end of X-cor INFO @ Fri, 10 Dec 2021 19:12:45: #2 finished! INFO @ Fri, 10 Dec 2021 19:12:45: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 19:12:45: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 19:12:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.10_model.r WARNING @ Fri, 10 Dec 2021 19:12:45: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:12:45: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 19:12:45: #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 19:12:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:12:50: 9000000 INFO @ Fri, 10 Dec 2021 19:12:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.10_summits.bed INFO @ Fri, 10 Dec 2021 19:12:55: Done! pass1 - making usageList (14 chroms): 2 millis BigWig に変換しました。 pass2 - checking and writing primary data (3168 records, 4 fields): 79 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:13:00: 10000000 INFO @ Fri, 10 Dec 2021 19:13:08: 11000000 INFO @ Fri, 10 Dec 2021 19:13:17: 12000000 INFO @ Fri, 10 Dec 2021 19:13:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:13:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:13:19: #1 total tags in treatment: 2466533 INFO @ Fri, 10 Dec 2021 19:13:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:13:19: #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 19:13:19: #1 tags after filtering in treatment: 2100763 INFO @ Fri, 10 Dec 2021 19:13:19: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 19:13:19: #1 finished! INFO @ Fri, 10 Dec 2021 19:13:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:13:19: #2 number of paired peaks: 4748 INFO @ Fri, 10 Dec 2021 19:13:19: start model_add_line... INFO @ Fri, 10 Dec 2021 19:13:19: start X-correlation... INFO @ Fri, 10 Dec 2021 19:13:19: end of X-cor INFO @ Fri, 10 Dec 2021 19:13:19: #2 finished! INFO @ Fri, 10 Dec 2021 19:13:19: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 19:13:19: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 19:13:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.20_model.r WARNING @ Fri, 10 Dec 2021 19:13:20: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:13:20: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 19:13:20: #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 19:13:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:13:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978845/ERX3978845.20_summits.bed INFO @ Fri, 10 Dec 2021 19:13:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 5 millis CompletedMACS2peakCalling