Job ID = 16439621 SRX = SRX11548848 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8394762 spots for SRR15243019/SRR15243019.sra Written 8394762 spots for SRR15243019/SRR15243019.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439734 ("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: 00:17:12 8394762 reads; of these: 8394762 (100.00%) were paired; of these: 1050929 (12.52%) aligned concordantly 0 times 5684004 (67.71%) aligned concordantly exactly 1 time 1659829 (19.77%) aligned concordantly >1 times ---- 1050929 pairs aligned concordantly 0 times; of these: 162663 (15.48%) aligned discordantly 1 time ---- 888266 pairs aligned 0 times concordantly or discordantly; of these: 1776532 mates make up the pairs; of these: 1367531 (76.98%) aligned 0 times 194346 (10.94%) aligned exactly 1 time 214655 (12.08%) aligned >1 times 91.85% overall alignment rate Time searching: 00:17:12 Overall time: 00:17:12 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] 277750 / 7498025 = 0.0370 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.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 @ Tue, 02 Aug 2022 16:06:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:06:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:06:17: 1000000 INFO @ Tue, 02 Aug 2022 16:06:23: 2000000 INFO @ Tue, 02 Aug 2022 16:06:29: 3000000 INFO @ Tue, 02 Aug 2022 16:06:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:06:41: 5000000 INFO @ Tue, 02 Aug 2022 16:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.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 @ Tue, 02 Aug 2022 16:06:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:06:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:06:47: 1000000 INFO @ Tue, 02 Aug 2022 16:06:47: 6000000 INFO @ Tue, 02 Aug 2022 16:06:52: 2000000 INFO @ Tue, 02 Aug 2022 16:06:54: 7000000 INFO @ Tue, 02 Aug 2022 16:06:58: 3000000 INFO @ Tue, 02 Aug 2022 16:07:00: 8000000 INFO @ Tue, 02 Aug 2022 16:07:04: 4000000 INFO @ Tue, 02 Aug 2022 16:07:06: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:07:10: 5000000 INFO @ Tue, 02 Aug 2022 16:07:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.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 @ Tue, 02 Aug 2022 16:07:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:07:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:07:13: 10000000 INFO @ Tue, 02 Aug 2022 16:07:15: 6000000 INFO @ Tue, 02 Aug 2022 16:07:17: 1000000 INFO @ Tue, 02 Aug 2022 16:07:19: 11000000 INFO @ Tue, 02 Aug 2022 16:07:21: 7000000 INFO @ Tue, 02 Aug 2022 16:07:24: 2000000 INFO @ Tue, 02 Aug 2022 16:07:25: 12000000 INFO @ Tue, 02 Aug 2022 16:07:27: 8000000 INFO @ Tue, 02 Aug 2022 16:07:30: 3000000 INFO @ Tue, 02 Aug 2022 16:07:31: 13000000 INFO @ Tue, 02 Aug 2022 16:07:32: 9000000 INFO @ Tue, 02 Aug 2022 16:07:36: 4000000 INFO @ Tue, 02 Aug 2022 16:07:38: 14000000 INFO @ Tue, 02 Aug 2022 16:07:38: 10000000 INFO @ Tue, 02 Aug 2022 16:07:43: 5000000 INFO @ Tue, 02 Aug 2022 16:07:43: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:07:43: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:07:43: #1 total tags in treatment: 7067540 INFO @ Tue, 02 Aug 2022 16:07:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:07:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:07:43: #1 tags after filtering in treatment: 6838099 INFO @ Tue, 02 Aug 2022 16:07:43: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:07:43: #1 finished! INFO @ Tue, 02 Aug 2022 16:07:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:07:44: 11000000 INFO @ Tue, 02 Aug 2022 16:07:44: #2 number of paired peaks: 108 WARNING @ Tue, 02 Aug 2022 16:07:44: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Tue, 02 Aug 2022 16:07:44: start model_add_line... INFO @ Tue, 02 Aug 2022 16:07:44: start X-correlation... INFO @ Tue, 02 Aug 2022 16:07:44: end of X-cor INFO @ Tue, 02 Aug 2022 16:07:44: #2 finished! INFO @ Tue, 02 Aug 2022 16:07:44: #2 predicted fragment length is 162 bps INFO @ Tue, 02 Aug 2022 16:07:44: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 02 Aug 2022 16:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.05_model.r INFO @ Tue, 02 Aug 2022 16:07:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:07:49: 6000000 INFO @ Tue, 02 Aug 2022 16:07:49: 12000000 INFO @ Tue, 02 Aug 2022 16:07:55: 13000000 INFO @ Tue, 02 Aug 2022 16:07:55: 7000000 INFO @ Tue, 02 Aug 2022 16:07:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:08:01: 14000000 INFO @ Tue, 02 Aug 2022 16:08:02: 8000000 INFO @ Tue, 02 Aug 2022 16:08:06: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:08:06: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:08:06: #1 total tags in treatment: 7067540 INFO @ Tue, 02 Aug 2022 16:08:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:08:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:08:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:08:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:08:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.05_summits.bed INFO @ Tue, 02 Aug 2022 16:08:06: Done! INFO @ Tue, 02 Aug 2022 16:08:06: #1 tags after filtering in treatment: 6838099 INFO @ Tue, 02 Aug 2022 16:08:06: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:08:06: #1 finished! INFO @ Tue, 02 Aug 2022 16:08:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:08:06: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 97 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:08:06: #2 number of paired peaks: 108 WARNING @ Tue, 02 Aug 2022 16:08:06: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Tue, 02 Aug 2022 16:08:06: start model_add_line... INFO @ Tue, 02 Aug 2022 16:08:06: start X-correlation... INFO @ Tue, 02 Aug 2022 16:08:06: end of X-cor INFO @ Tue, 02 Aug 2022 16:08:06: #2 finished! INFO @ Tue, 02 Aug 2022 16:08:06: #2 predicted fragment length is 162 bps INFO @ Tue, 02 Aug 2022 16:08:06: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 02 Aug 2022 16:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.10_model.r INFO @ Tue, 02 Aug 2022 16:08:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:08:08: 9000000 INFO @ Tue, 02 Aug 2022 16:08:14: 10000000 INFO @ Tue, 02 Aug 2022 16:08:20: 11000000 INFO @ Tue, 02 Aug 2022 16:08:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:08:26: 12000000 INFO @ Tue, 02 Aug 2022 16:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.10_summits.bed INFO @ Tue, 02 Aug 2022 16:08:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:08:32: 13000000 INFO @ Tue, 02 Aug 2022 16:08:39: 14000000 INFO @ Tue, 02 Aug 2022 16:08:44: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:08:44: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:08:44: #1 total tags in treatment: 7067540 INFO @ Tue, 02 Aug 2022 16:08:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:08:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:08:44: #1 tags after filtering in treatment: 6838099 INFO @ Tue, 02 Aug 2022 16:08:44: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 16:08:44: #1 finished! INFO @ Tue, 02 Aug 2022 16:08:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:08:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:08:44: #2 number of paired peaks: 108 WARNING @ Tue, 02 Aug 2022 16:08:44: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Tue, 02 Aug 2022 16:08:44: start model_add_line... INFO @ Tue, 02 Aug 2022 16:08:44: start X-correlation... INFO @ Tue, 02 Aug 2022 16:08:44: end of X-cor INFO @ Tue, 02 Aug 2022 16:08:44: #2 finished! INFO @ Tue, 02 Aug 2022 16:08:44: #2 predicted fragment length is 162 bps INFO @ Tue, 02 Aug 2022 16:08:44: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 02 Aug 2022 16:08:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.20_model.r INFO @ Tue, 02 Aug 2022 16:08:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:08:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:08:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11548848/SRX11548848.20_summits.bed INFO @ Tue, 02 Aug 2022 16:09:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 19 millis CompletedMACS2peakCalling