Job ID = 12265323 SRX = SRX5736452 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20988596 spots for SRR8956863/SRR8956863.sra Written 20988596 spots for SRR8956863/SRR8956863.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265549 ("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: 00:24:35 20988596 reads; of these: 20988596 (100.00%) were paired; of these: 13032276 (62.09%) aligned concordantly 0 times 4727344 (22.52%) aligned concordantly exactly 1 time 3228976 (15.38%) aligned concordantly >1 times ---- 13032276 pairs aligned concordantly 0 times; of these: 451976 (3.47%) aligned discordantly 1 time ---- 12580300 pairs aligned 0 times concordantly or discordantly; of these: 25160600 mates make up the pairs; of these: 24068768 (95.66%) aligned 0 times 180526 (0.72%) aligned exactly 1 time 911306 (3.62%) aligned >1 times 42.66% overall alignment rate Time searching: 00:24:35 Overall time: 00:24:35 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] 2181121 / 8326172 = 0.2620 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 07:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.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 07:08:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:08:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:08:49: 1000000 INFO @ Sat, 03 Apr 2021 07:08:55: 2000000 INFO @ Sat, 03 Apr 2021 07:09:01: 3000000 INFO @ Sat, 03 Apr 2021 07:09:06: 4000000 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 07:09:12: 5000000 INFO @ Sat, 03 Apr 2021 07:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.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 07:09:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:09:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:09:18: 6000000 INFO @ Sat, 03 Apr 2021 07:09:19: 1000000 INFO @ Sat, 03 Apr 2021 07:09:23: 7000000 INFO @ Sat, 03 Apr 2021 07:09:24: 2000000 INFO @ Sat, 03 Apr 2021 07:09:29: 8000000 INFO @ Sat, 03 Apr 2021 07:09:30: 3000000 INFO @ Sat, 03 Apr 2021 07:09:35: 9000000 INFO @ Sat, 03 Apr 2021 07:09:36: 4000000 INFO @ Sat, 03 Apr 2021 07:09:40: 10000000 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 07:09:42: 5000000 INFO @ Sat, 03 Apr 2021 07:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.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 07:09:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:09:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:09:46: 11000000 INFO @ Sat, 03 Apr 2021 07:09:48: 6000000 INFO @ Sat, 03 Apr 2021 07:09:49: 1000000 INFO @ Sat, 03 Apr 2021 07:09:51: 12000000 INFO @ Sat, 03 Apr 2021 07:09:54: 7000000 INFO @ Sat, 03 Apr 2021 07:09:55: 2000000 INFO @ Sat, 03 Apr 2021 07:09:57: 13000000 INFO @ Sat, 03 Apr 2021 07:10:00: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:10:00: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:10:00: #1 total tags in treatment: 5807729 INFO @ Sat, 03 Apr 2021 07:10:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:10:00: #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 07:10:00: 8000000 INFO @ Sat, 03 Apr 2021 07:10:00: #1 tags after filtering in treatment: 4888614 INFO @ Sat, 03 Apr 2021 07:10:00: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 07:10:00: #1 finished! INFO @ Sat, 03 Apr 2021 07:10:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:10:01: 3000000 INFO @ Sat, 03 Apr 2021 07:10:01: #2 number of paired peaks: 1226 INFO @ Sat, 03 Apr 2021 07:10:01: start model_add_line... INFO @ Sat, 03 Apr 2021 07:10:01: start X-correlation... INFO @ Sat, 03 Apr 2021 07:10:01: end of X-cor INFO @ Sat, 03 Apr 2021 07:10:01: #2 finished! INFO @ Sat, 03 Apr 2021 07:10:01: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Apr 2021 07:10:01: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 03 Apr 2021 07:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.05_model.r WARNING @ Sat, 03 Apr 2021 07:10:01: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:10:01: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sat, 03 Apr 2021 07:10:01: #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 07:10:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:10:06: 9000000 INFO @ Sat, 03 Apr 2021 07:10:07: 4000000 INFO @ Sat, 03 Apr 2021 07:10:12: 10000000 INFO @ Sat, 03 Apr 2021 07:10:13: 5000000 INFO @ Sat, 03 Apr 2021 07:10:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:10:18: 11000000 INFO @ Sat, 03 Apr 2021 07:10:19: 6000000 INFO @ Sat, 03 Apr 2021 07:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.05_summits.bed INFO @ Sat, 03 Apr 2021 07:10:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4530 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:10:25: 12000000 INFO @ Sat, 03 Apr 2021 07:10:26: 7000000 INFO @ Sat, 03 Apr 2021 07:10:31: 13000000 INFO @ Sat, 03 Apr 2021 07:10:32: 8000000 INFO @ Sat, 03 Apr 2021 07:10:34: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:10:34: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:10:34: #1 total tags in treatment: 5807729 INFO @ Sat, 03 Apr 2021 07:10:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:10:34: #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 07:10:34: #1 tags after filtering in treatment: 4888614 INFO @ Sat, 03 Apr 2021 07:10:34: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 07:10:34: #1 finished! INFO @ Sat, 03 Apr 2021 07:10:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:10:34: #2 number of paired peaks: 1226 INFO @ Sat, 03 Apr 2021 07:10:34: start model_add_line... INFO @ Sat, 03 Apr 2021 07:10:34: start X-correlation... INFO @ Sat, 03 Apr 2021 07:10:35: end of X-cor INFO @ Sat, 03 Apr 2021 07:10:35: #2 finished! INFO @ Sat, 03 Apr 2021 07:10:35: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Apr 2021 07:10:35: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 03 Apr 2021 07:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.10_model.r WARNING @ Sat, 03 Apr 2021 07:10:35: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:10:35: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sat, 03 Apr 2021 07:10:35: #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 07:10:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:10:37: 9000000 INFO @ Sat, 03 Apr 2021 07:10:43: 10000000 INFO @ Sat, 03 Apr 2021 07:10:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:10:49: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.10_summits.bed INFO @ Sat, 03 Apr 2021 07:10:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2471 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:10:55: 12000000 INFO @ Sat, 03 Apr 2021 07:11:01: 13000000 INFO @ Sat, 03 Apr 2021 07:11:04: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:11:04: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:11:04: #1 total tags in treatment: 5807729 INFO @ Sat, 03 Apr 2021 07:11:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:11:04: #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 07:11:04: #1 tags after filtering in treatment: 4888614 INFO @ Sat, 03 Apr 2021 07:11:04: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 03 Apr 2021 07:11:04: #1 finished! INFO @ Sat, 03 Apr 2021 07:11:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:11:04: #2 number of paired peaks: 1226 INFO @ Sat, 03 Apr 2021 07:11:04: start model_add_line... INFO @ Sat, 03 Apr 2021 07:11:04: start X-correlation... INFO @ Sat, 03 Apr 2021 07:11:04: end of X-cor INFO @ Sat, 03 Apr 2021 07:11:04: #2 finished! INFO @ Sat, 03 Apr 2021 07:11:04: #2 predicted fragment length is 140 bps INFO @ Sat, 03 Apr 2021 07:11:04: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 03 Apr 2021 07:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.20_model.r WARNING @ Sat, 03 Apr 2021 07:11:05: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:11:05: #2 You may need to consider one of the other alternative d(s): 140 WARNING @ Sat, 03 Apr 2021 07:11:05: #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 07:11:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:11:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736452/SRX5736452.20_summits.bed INFO @ Sat, 03 Apr 2021 07:11:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1031 records, 4 fields): 3 millis CompletedMACS2peakCalling