Job ID = 14168272 SRX = ERX3978847 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9818972 spots for ERR3975916/ERR3975916.sra Written 9818972 spots for ERR3975916/ERR3975916.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169284 ("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: 00:24:14 9818972 reads; of these: 9818972 (100.00%) were paired; of these: 1349345 (13.74%) aligned concordantly 0 times 6458283 (65.77%) aligned concordantly exactly 1 time 2011344 (20.48%) aligned concordantly >1 times ---- 1349345 pairs aligned concordantly 0 times; of these: 163401 (12.11%) aligned discordantly 1 time ---- 1185944 pairs aligned 0 times concordantly or discordantly; of these: 2371888 mates make up the pairs; of these: 1518452 (64.02%) aligned 0 times 396531 (16.72%) aligned exactly 1 time 456905 (19.26%) aligned >1 times 92.27% overall alignment rate Time searching: 00:24:14 Overall time: 00:24:14 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 8 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] 5233873 / 8596166 = 0.6089 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 17:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.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 17:15:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:15:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:15:32: 1000000 INFO @ Fri, 10 Dec 2021 17:15:40: 2000000 INFO @ Fri, 10 Dec 2021 17:15:49: 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 17:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.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 17:15:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:15:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:15:57: 4000000 INFO @ Fri, 10 Dec 2021 17:16:03: 1000000 INFO @ Fri, 10 Dec 2021 17:16:05: 5000000 INFO @ Fri, 10 Dec 2021 17:16:12: 2000000 INFO @ Fri, 10 Dec 2021 17:16:14: 6000000 INFO @ Fri, 10 Dec 2021 17:16:21: 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 17:16:23: 7000000 INFO @ Fri, 10 Dec 2021 17:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.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 17:16:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:16:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:16:28: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:16:28: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:16:28: #1 total tags in treatment: 3335949 INFO @ Fri, 10 Dec 2021 17:16:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:16:28: #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 17:16:28: #1 tags after filtering in treatment: 3132737 INFO @ Fri, 10 Dec 2021 17:16:28: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 17:16:28: #1 finished! INFO @ Fri, 10 Dec 2021 17:16:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:16:29: #2 number of paired peaks: 1020 INFO @ Fri, 10 Dec 2021 17:16:29: start model_add_line... INFO @ Fri, 10 Dec 2021 17:16:29: start X-correlation... INFO @ Fri, 10 Dec 2021 17:16:29: end of X-cor INFO @ Fri, 10 Dec 2021 17:16:29: #2 finished! INFO @ Fri, 10 Dec 2021 17:16:29: #2 predicted fragment length is 140 bps INFO @ Fri, 10 Dec 2021 17:16:29: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 10 Dec 2021 17:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.05_model.r WARNING @ Fri, 10 Dec 2021 17:16:29: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:16:29: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Fri, 10 Dec 2021 17:16:29: #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 17:16:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:16:30: 4000000 INFO @ Fri, 10 Dec 2021 17:16:33: 1000000 INFO @ Fri, 10 Dec 2021 17:16:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:16:38: 5000000 INFO @ Fri, 10 Dec 2021 17:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.05_summits.bed INFO @ Fri, 10 Dec 2021 17:16:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2331 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:16:42: 2000000 INFO @ Fri, 10 Dec 2021 17:16:47: 6000000 INFO @ Fri, 10 Dec 2021 17:16:51: 3000000 INFO @ Fri, 10 Dec 2021 17:16:56: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:16:59: 4000000 INFO @ Fri, 10 Dec 2021 17:17:01: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:17:01: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:17:01: #1 total tags in treatment: 3335949 INFO @ Fri, 10 Dec 2021 17:17:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:17:01: #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 17:17:01: #1 tags after filtering in treatment: 3132737 INFO @ Fri, 10 Dec 2021 17:17:01: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 17:17:01: #1 finished! INFO @ Fri, 10 Dec 2021 17:17:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:17:01: #2 number of paired peaks: 1020 INFO @ Fri, 10 Dec 2021 17:17:01: start model_add_line... INFO @ Fri, 10 Dec 2021 17:17:01: start X-correlation... INFO @ Fri, 10 Dec 2021 17:17:01: end of X-cor INFO @ Fri, 10 Dec 2021 17:17:01: #2 finished! INFO @ Fri, 10 Dec 2021 17:17:01: #2 predicted fragment length is 140 bps INFO @ Fri, 10 Dec 2021 17:17:01: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 10 Dec 2021 17:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.10_model.r WARNING @ Fri, 10 Dec 2021 17:17:01: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:17:01: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Fri, 10 Dec 2021 17:17:01: #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 17:17:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:17:08: 5000000 INFO @ Fri, 10 Dec 2021 17:17:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.10_summits.bed INFO @ Fri, 10 Dec 2021 17:17:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:17:16: 6000000 INFO @ Fri, 10 Dec 2021 17:17:24: 7000000 INFO @ Fri, 10 Dec 2021 17:17:29: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:17:29: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:17:29: #1 total tags in treatment: 3335949 INFO @ Fri, 10 Dec 2021 17:17:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:17:29: #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 17:17:29: #1 tags after filtering in treatment: 3132737 INFO @ Fri, 10 Dec 2021 17:17:29: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 17:17:29: #1 finished! INFO @ Fri, 10 Dec 2021 17:17:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:17:29: #2 number of paired peaks: 1020 INFO @ Fri, 10 Dec 2021 17:17:29: start model_add_line... INFO @ Fri, 10 Dec 2021 17:17:29: start X-correlation... INFO @ Fri, 10 Dec 2021 17:17:29: end of X-cor INFO @ Fri, 10 Dec 2021 17:17:29: #2 finished! INFO @ Fri, 10 Dec 2021 17:17:29: #2 predicted fragment length is 140 bps INFO @ Fri, 10 Dec 2021 17:17:29: #2 alternative fragment length(s) may be 140 bps INFO @ Fri, 10 Dec 2021 17:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.20_model.r WARNING @ Fri, 10 Dec 2021 17:17:29: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:17:29: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Fri, 10 Dec 2021 17:17:29: #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 17:17:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:17:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978847/ERX3978847.20_summits.bed INFO @ Fri, 10 Dec 2021 17:17:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (486 records, 4 fields): 2 millis CompletedMACS2peakCalling