Job ID = 14168211 SRX = ERX3978955 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18125773 spots for ERR3976026/ERR3976026.sra Written 18125773 spots for ERR3976026/ERR3976026.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169460 ("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: 01:35:07 18125773 reads; of these: 18125773 (100.00%) were paired; of these: 6226849 (34.35%) aligned concordantly 0 times 8527603 (47.05%) aligned concordantly exactly 1 time 3371321 (18.60%) aligned concordantly >1 times ---- 6226849 pairs aligned concordantly 0 times; of these: 407659 (6.55%) aligned discordantly 1 time ---- 5819190 pairs aligned 0 times concordantly or discordantly; of these: 11638380 mates make up the pairs; of these: 5474825 (47.04%) aligned 0 times 3355352 (28.83%) aligned exactly 1 time 2808203 (24.13%) aligned >1 times 84.90% overall alignment rate Time searching: 01:35:07 Overall time: 01:35:07 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 16 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] 9628738 / 12168800 = 0.7913 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 17:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.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 17:53:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:53:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:53:19: 1000000 INFO @ Fri, 10 Dec 2021 17:53:27: 2000000 INFO @ Fri, 10 Dec 2021 17:53:34: 3000000 INFO @ Fri, 10 Dec 2021 17:53:40: 4000000 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 17:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.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 17:53:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:53:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:53:47: 5000000 INFO @ Fri, 10 Dec 2021 17:53:50: 1000000 INFO @ Fri, 10 Dec 2021 17:53:54: 6000000 INFO @ Fri, 10 Dec 2021 17:53:57: 2000000 INFO @ Fri, 10 Dec 2021 17:54:01: 7000000 INFO @ Fri, 10 Dec 2021 17:54:04: 3000000 INFO @ Fri, 10 Dec 2021 17:54:08: 8000000 INFO @ Fri, 10 Dec 2021 17:54:11: 4000000 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 17:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.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 17:54:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:54:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:54:15: 9000000 INFO @ Fri, 10 Dec 2021 17:54:18: 5000000 INFO @ Fri, 10 Dec 2021 17:54:21: 1000000 INFO @ Fri, 10 Dec 2021 17:54:23: 10000000 INFO @ Fri, 10 Dec 2021 17:54:25: 6000000 INFO @ Fri, 10 Dec 2021 17:54:29: 2000000 INFO @ Fri, 10 Dec 2021 17:54:30: 11000000 INFO @ Fri, 10 Dec 2021 17:54:32: 7000000 INFO @ Fri, 10 Dec 2021 17:54:34: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:54:34: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:54:34: #1 total tags in treatment: 2544069 INFO @ Fri, 10 Dec 2021 17:54:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:54:34: #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 17:54:34: #1 tags after filtering in treatment: 2162974 INFO @ Fri, 10 Dec 2021 17:54:34: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:54:34: #1 finished! INFO @ Fri, 10 Dec 2021 17:54:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:54:35: #2 number of paired peaks: 3829 INFO @ Fri, 10 Dec 2021 17:54:35: start model_add_line... INFO @ Fri, 10 Dec 2021 17:54:35: start X-correlation... INFO @ Fri, 10 Dec 2021 17:54:35: end of X-cor INFO @ Fri, 10 Dec 2021 17:54:35: #2 finished! INFO @ Fri, 10 Dec 2021 17:54:35: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 17:54:35: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 17:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.05_model.r WARNING @ Fri, 10 Dec 2021 17:54:35: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:54:35: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Fri, 10 Dec 2021 17:54:35: #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 17:54:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:54:37: 3000000 INFO @ Fri, 10 Dec 2021 17:54:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:54:40: 8000000 INFO @ Fri, 10 Dec 2021 17:54:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:54:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:54:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.05_summits.bed INFO @ Fri, 10 Dec 2021 17:54:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5301 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:54:45: 4000000 INFO @ Fri, 10 Dec 2021 17:54:47: 9000000 INFO @ Fri, 10 Dec 2021 17:54:53: 5000000 INFO @ Fri, 10 Dec 2021 17:54:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:55:00: 6000000 INFO @ Fri, 10 Dec 2021 17:55:02: 11000000 INFO @ Fri, 10 Dec 2021 17:55:06: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:55:06: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:55:06: #1 total tags in treatment: 2544069 INFO @ Fri, 10 Dec 2021 17:55:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:55:06: #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 17:55:06: #1 tags after filtering in treatment: 2162974 INFO @ Fri, 10 Dec 2021 17:55:06: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:55:06: #1 finished! INFO @ Fri, 10 Dec 2021 17:55:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:55:06: #2 number of paired peaks: 3829 INFO @ Fri, 10 Dec 2021 17:55:06: start model_add_line... INFO @ Fri, 10 Dec 2021 17:55:06: start X-correlation... INFO @ Fri, 10 Dec 2021 17:55:06: end of X-cor INFO @ Fri, 10 Dec 2021 17:55:06: #2 finished! INFO @ Fri, 10 Dec 2021 17:55:06: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 17:55:06: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 17:55:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.10_model.r WARNING @ Fri, 10 Dec 2021 17:55:06: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:55:06: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Fri, 10 Dec 2021 17:55:06: #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 17:55:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:55:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:55:07: 7000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:55:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.10_summits.bed INFO @ Fri, 10 Dec 2021 17:55:13: Done! INFO @ Fri, 10 Dec 2021 17:55:14: 8000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1975 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:55:20: 9000000 INFO @ Fri, 10 Dec 2021 17:55:26: 10000000 INFO @ Fri, 10 Dec 2021 17:55:32: 11000000 INFO @ Fri, 10 Dec 2021 17:55:35: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:55:35: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:55:35: #1 total tags in treatment: 2544069 INFO @ Fri, 10 Dec 2021 17:55:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:55:35: #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 17:55:36: #1 tags after filtering in treatment: 2162974 INFO @ Fri, 10 Dec 2021 17:55:36: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:55:36: #1 finished! INFO @ Fri, 10 Dec 2021 17:55:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:55:36: #2 number of paired peaks: 3829 INFO @ Fri, 10 Dec 2021 17:55:36: start model_add_line... INFO @ Fri, 10 Dec 2021 17:55:36: start X-correlation... INFO @ Fri, 10 Dec 2021 17:55:36: end of X-cor INFO @ Fri, 10 Dec 2021 17:55:36: #2 finished! INFO @ Fri, 10 Dec 2021 17:55:36: #2 predicted fragment length is 151 bps INFO @ Fri, 10 Dec 2021 17:55:36: #2 alternative fragment length(s) may be 151 bps INFO @ Fri, 10 Dec 2021 17:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.20_model.r WARNING @ Fri, 10 Dec 2021 17:55:36: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:55:36: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Fri, 10 Dec 2021 17:55:36: #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 17:55:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:55:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978955/ERX3978955.20_summits.bed INFO @ Fri, 10 Dec 2021 17:55:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 2 millis CompletedMACS2peakCalling