Job ID = 12266688 SRX = SRX8622123 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36814531 spots for SRR12096683/SRR12096683.sra Written 36814531 spots for SRR12096683/SRR12096683.sra fastq に変換しました。 bowtie でマッピング中... Your job 12268483 ("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: 01:19:19 36814531 reads; of these: 36814531 (100.00%) were paired; of these: 33466373 (90.91%) aligned concordantly 0 times 2184047 (5.93%) aligned concordantly exactly 1 time 1164111 (3.16%) aligned concordantly >1 times ---- 33466373 pairs aligned concordantly 0 times; of these: 1201533 (3.59%) aligned discordantly 1 time ---- 32264840 pairs aligned 0 times concordantly or discordantly; of these: 64529680 mates make up the pairs; of these: 63207275 (97.95%) aligned 0 times 360654 (0.56%) aligned exactly 1 time 961751 (1.49%) aligned >1 times 14.15% overall alignment rate Time searching: 01:19:19 Overall time: 01:19:19 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] 762331 / 4486495 = 0.1699 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.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 @ Sat, 03 Apr 2021 10:45:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:45:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:45:11: 1000000 INFO @ Sat, 03 Apr 2021 10:45:20: 2000000 INFO @ Sat, 03 Apr 2021 10:45:29: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.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 @ Sat, 03 Apr 2021 10:45:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:45:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:45:39: 4000000 INFO @ Sat, 03 Apr 2021 10:45:43: 1000000 INFO @ Sat, 03 Apr 2021 10:45:48: 5000000 INFO @ Sat, 03 Apr 2021 10:45:52: 2000000 INFO @ Sat, 03 Apr 2021 10:45:57: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:46:02: 3000000 INFO @ Sat, 03 Apr 2021 10:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.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 @ Sat, 03 Apr 2021 10:46:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:46:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:46:08: 7000000 INFO @ Sat, 03 Apr 2021 10:46:11: 4000000 INFO @ Sat, 03 Apr 2021 10:46:12: 1000000 INFO @ Sat, 03 Apr 2021 10:46:18: 8000000 INFO @ Sat, 03 Apr 2021 10:46:22: 2000000 INFO @ Sat, 03 Apr 2021 10:46:22: 5000000 INFO @ Sat, 03 Apr 2021 10:46:27: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:46:27: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:46:27: #1 total tags in treatment: 2763208 INFO @ Sat, 03 Apr 2021 10:46:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:46:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:46:27: #1 tags after filtering in treatment: 2417677 INFO @ Sat, 03 Apr 2021 10:46:27: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 10:46:27: #1 finished! INFO @ Sat, 03 Apr 2021 10:46:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:46:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:46:27: #2 number of paired peaks: 2051 INFO @ Sat, 03 Apr 2021 10:46:27: start model_add_line... INFO @ Sat, 03 Apr 2021 10:46:28: start X-correlation... INFO @ Sat, 03 Apr 2021 10:46:28: end of X-cor INFO @ Sat, 03 Apr 2021 10:46:28: #2 finished! INFO @ Sat, 03 Apr 2021 10:46:28: #2 predicted fragment length is 188 bps INFO @ Sat, 03 Apr 2021 10:46:28: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 03 Apr 2021 10:46:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.05_model.r WARNING @ Sat, 03 Apr 2021 10:46:28: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:46:28: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Sat, 03 Apr 2021 10:46:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:46:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:46:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:46:32: 3000000 INFO @ Sat, 03 Apr 2021 10:46:32: 6000000 INFO @ Sat, 03 Apr 2021 10:46:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.05_peaks.xls INFO @ Sat, 03 Apr 2021 10:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:46:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.05_summits.bed INFO @ Sat, 03 Apr 2021 10:46:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3970 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:46:40: 4000000 INFO @ Sat, 03 Apr 2021 10:46:42: 7000000 INFO @ Sat, 03 Apr 2021 10:46:49: 5000000 INFO @ Sat, 03 Apr 2021 10:46:53: 8000000 INFO @ Sat, 03 Apr 2021 10:46:59: 6000000 INFO @ Sat, 03 Apr 2021 10:47:01: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:47:01: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:47:01: #1 total tags in treatment: 2763208 INFO @ Sat, 03 Apr 2021 10:47:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:47:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:47:01: #1 tags after filtering in treatment: 2417677 INFO @ Sat, 03 Apr 2021 10:47:01: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 10:47:01: #1 finished! INFO @ Sat, 03 Apr 2021 10:47:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:47:01: #2 number of paired peaks: 2051 INFO @ Sat, 03 Apr 2021 10:47:01: start model_add_line... INFO @ Sat, 03 Apr 2021 10:47:01: start X-correlation... INFO @ Sat, 03 Apr 2021 10:47:01: end of X-cor INFO @ Sat, 03 Apr 2021 10:47:01: #2 finished! INFO @ Sat, 03 Apr 2021 10:47:01: #2 predicted fragment length is 188 bps INFO @ Sat, 03 Apr 2021 10:47:01: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 03 Apr 2021 10:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.10_model.r WARNING @ Sat, 03 Apr 2021 10:47:01: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:47:01: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Sat, 03 Apr 2021 10:47:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:47:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:47:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:47:07: 7000000 INFO @ Sat, 03 Apr 2021 10:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.10_summits.bed INFO @ Sat, 03 Apr 2021 10:47:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1721 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 10:47:16: 8000000 INFO @ Sat, 03 Apr 2021 10:47:24: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 10:47:24: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 10:47:24: #1 total tags in treatment: 2763208 INFO @ Sat, 03 Apr 2021 10:47:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:47:25: #1 tags after filtering in treatment: 2417677 INFO @ Sat, 03 Apr 2021 10:47:25: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 10:47:25: #1 finished! INFO @ Sat, 03 Apr 2021 10:47:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:47:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:47:25: #2 number of paired peaks: 2051 INFO @ Sat, 03 Apr 2021 10:47:25: start model_add_line... INFO @ Sat, 03 Apr 2021 10:47:25: start X-correlation... INFO @ Sat, 03 Apr 2021 10:47:25: end of X-cor INFO @ Sat, 03 Apr 2021 10:47:25: #2 finished! INFO @ Sat, 03 Apr 2021 10:47:25: #2 predicted fragment length is 188 bps INFO @ Sat, 03 Apr 2021 10:47:25: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 03 Apr 2021 10:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.20_model.r WARNING @ Sat, 03 Apr 2021 10:47:25: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:47:25: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Sat, 03 Apr 2021 10:47:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:47:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:47:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622123/SRX8622123.20_summits.bed INFO @ Sat, 03 Apr 2021 10:47:33: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (533 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。