Job ID = 14166959 SRX = SRX7541124 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8619744 spots for SRR10871146/SRR10871146.sra Written 8619744 spots for SRR10871146/SRR10871146.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167328 ("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: 00:31:03 8619744 reads; of these: 8619744 (100.00%) were paired; of these: 1655722 (19.21%) aligned concordantly 0 times 5311046 (61.61%) aligned concordantly exactly 1 time 1652976 (19.18%) aligned concordantly >1 times ---- 1655722 pairs aligned concordantly 0 times; of these: 532898 (32.19%) aligned discordantly 1 time ---- 1122824 pairs aligned 0 times concordantly or discordantly; of these: 2245648 mates make up the pairs; of these: 1054549 (46.96%) aligned 0 times 505022 (22.49%) aligned exactly 1 time 686077 (30.55%) aligned >1 times 93.88% overall alignment rate Time searching: 00:31:03 Overall time: 00:31:03 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] 3730713 / 7485665 = 0.4984 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 08:43:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.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 08:43:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:43:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:43:15: 1000000 INFO @ Fri, 10 Dec 2021 08:43:22: 2000000 INFO @ Fri, 10 Dec 2021 08:43:29: 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 08:43:36: 4000000 INFO @ Fri, 10 Dec 2021 08:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.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 08:43:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:43:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:43:43: 5000000 INFO @ Fri, 10 Dec 2021 08:43:44: 1000000 INFO @ Fri, 10 Dec 2021 08:43:51: 6000000 INFO @ Fri, 10 Dec 2021 08:43:52: 2000000 INFO @ Fri, 10 Dec 2021 08:43:59: 7000000 INFO @ Fri, 10 Dec 2021 08:43:59: 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 08:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.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 08:44:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:44:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:44:07: 8000000 INFO @ Fri, 10 Dec 2021 08:44:07: 4000000 INFO @ Fri, 10 Dec 2021 08:44:13: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:44:13: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:44:13: #1 total tags in treatment: 3381855 INFO @ Fri, 10 Dec 2021 08:44:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:44:13: #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 08:44:13: #1 tags after filtering in treatment: 3174448 INFO @ Fri, 10 Dec 2021 08:44:13: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 08:44:13: #1 finished! INFO @ Fri, 10 Dec 2021 08:44:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:44:13: #2 number of paired peaks: 1084 INFO @ Fri, 10 Dec 2021 08:44:13: start model_add_line... INFO @ Fri, 10 Dec 2021 08:44:13: start X-correlation... INFO @ Fri, 10 Dec 2021 08:44:13: end of X-cor INFO @ Fri, 10 Dec 2021 08:44:13: #2 finished! INFO @ Fri, 10 Dec 2021 08:44:13: #2 predicted fragment length is 159 bps INFO @ Fri, 10 Dec 2021 08:44:13: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 10 Dec 2021 08:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.05_model.r WARNING @ Fri, 10 Dec 2021 08:44:13: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:44:13: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Fri, 10 Dec 2021 08:44:13: #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 08:44:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:44:14: 1000000 INFO @ Fri, 10 Dec 2021 08:44:15: 5000000 INFO @ Fri, 10 Dec 2021 08:44:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:44:21: 2000000 INFO @ Fri, 10 Dec 2021 08:44:22: 6000000 INFO @ Fri, 10 Dec 2021 08:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.05_summits.bed INFO @ Fri, 10 Dec 2021 08:44:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2651 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:44:29: 3000000 INFO @ Fri, 10 Dec 2021 08:44:30: 7000000 INFO @ Fri, 10 Dec 2021 08:44:36: 4000000 INFO @ Fri, 10 Dec 2021 08:44:37: 8000000 INFO @ Fri, 10 Dec 2021 08:44:42: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:44:42: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:44:42: #1 total tags in treatment: 3381855 INFO @ Fri, 10 Dec 2021 08:44:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:44:42: #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 08:44:42: #1 tags after filtering in treatment: 3174448 INFO @ Fri, 10 Dec 2021 08:44:42: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 08:44:42: #1 finished! INFO @ Fri, 10 Dec 2021 08:44:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:44:43: #2 number of paired peaks: 1084 INFO @ Fri, 10 Dec 2021 08:44:43: start model_add_line... INFO @ Fri, 10 Dec 2021 08:44:43: start X-correlation... INFO @ Fri, 10 Dec 2021 08:44:43: end of X-cor INFO @ Fri, 10 Dec 2021 08:44:43: #2 finished! INFO @ Fri, 10 Dec 2021 08:44:43: #2 predicted fragment length is 159 bps INFO @ Fri, 10 Dec 2021 08:44:43: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 10 Dec 2021 08:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.10_model.r WARNING @ Fri, 10 Dec 2021 08:44:43: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:44:43: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Fri, 10 Dec 2021 08:44:43: #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 08:44:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:44:44: 5000000 INFO @ Fri, 10 Dec 2021 08:44:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:44:51: 6000000 INFO @ Fri, 10 Dec 2021 08:44:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:44:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:44:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.10_summits.bed INFO @ Fri, 10 Dec 2021 08:44:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:44:58: 7000000 INFO @ Fri, 10 Dec 2021 08:45:05: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:45:11: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:45:11: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:45:11: #1 total tags in treatment: 3381855 INFO @ Fri, 10 Dec 2021 08:45:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:45:11: #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 08:45:11: #1 tags after filtering in treatment: 3174448 INFO @ Fri, 10 Dec 2021 08:45:11: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 08:45:11: #1 finished! INFO @ Fri, 10 Dec 2021 08:45:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:45:11: #2 number of paired peaks: 1084 INFO @ Fri, 10 Dec 2021 08:45:11: start model_add_line... INFO @ Fri, 10 Dec 2021 08:45:11: start X-correlation... INFO @ Fri, 10 Dec 2021 08:45:11: end of X-cor INFO @ Fri, 10 Dec 2021 08:45:11: #2 finished! INFO @ Fri, 10 Dec 2021 08:45:11: #2 predicted fragment length is 159 bps INFO @ Fri, 10 Dec 2021 08:45:11: #2 alternative fragment length(s) may be 159 bps INFO @ Fri, 10 Dec 2021 08:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.20_model.r WARNING @ Fri, 10 Dec 2021 08:45:12: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:45:12: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Fri, 10 Dec 2021 08:45:12: #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 08:45:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:45:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:45:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541124/SRX7541124.20_summits.bed INFO @ Fri, 10 Dec 2021 08:45:22: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (524 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。