Job ID = 14168818 SRX = ERX3978777 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20302237 spots for ERR3975798/ERR3975798.sra Written 20302237 spots for ERR3975798/ERR3975798.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169903 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:38:58 20302237 reads; of these: 20302237 (100.00%) were paired; of these: 7399474 (36.45%) aligned concordantly 0 times 4320167 (21.28%) aligned concordantly exactly 1 time 8582596 (42.27%) aligned concordantly >1 times ---- 7399474 pairs aligned concordantly 0 times; of these: 1491201 (20.15%) aligned discordantly 1 time ---- 5908273 pairs aligned 0 times concordantly or discordantly; of these: 11816546 mates make up the pairs; of these: 6537202 (55.32%) aligned 0 times 314853 (2.66%) aligned exactly 1 time 4964491 (42.01%) aligned >1 times 83.90% overall alignment rate Time searching: 00:38:59 Overall time: 00:38:59 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 24 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] 6908858 / 14284336 = 0.4837 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 21:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.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 21:27:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:27:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:27:46: 1000000 INFO @ Fri, 10 Dec 2021 21:27:54: 2000000 INFO @ Fri, 10 Dec 2021 21:28:02: 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 21:28:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.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 21:28:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:28:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:28:09: 4000000 INFO @ Fri, 10 Dec 2021 21:28:15: 1000000 INFO @ Fri, 10 Dec 2021 21:28:17: 5000000 INFO @ Fri, 10 Dec 2021 21:28:23: 2000000 INFO @ Fri, 10 Dec 2021 21:28:26: 6000000 INFO @ Fri, 10 Dec 2021 21:28:29: 3000000 INFO @ Fri, 10 Dec 2021 21:28:34: 7000000 INFO @ Fri, 10 Dec 2021 21:28:37: 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 21:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.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 21:28:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:28:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:28:42: 8000000 INFO @ Fri, 10 Dec 2021 21:28:44: 5000000 INFO @ Fri, 10 Dec 2021 21:28:46: 1000000 INFO @ Fri, 10 Dec 2021 21:28:50: 9000000 INFO @ Fri, 10 Dec 2021 21:28:51: 6000000 INFO @ Fri, 10 Dec 2021 21:28:53: 2000000 INFO @ Fri, 10 Dec 2021 21:28:58: 10000000 INFO @ Fri, 10 Dec 2021 21:28:58: 7000000 INFO @ Fri, 10 Dec 2021 21:29:00: 3000000 INFO @ Fri, 10 Dec 2021 21:29:05: 8000000 INFO @ Fri, 10 Dec 2021 21:29:06: 11000000 INFO @ Fri, 10 Dec 2021 21:29:07: 4000000 INFO @ Fri, 10 Dec 2021 21:29:12: 9000000 INFO @ Fri, 10 Dec 2021 21:29:13: 12000000 INFO @ Fri, 10 Dec 2021 21:29:14: 5000000 INFO @ Fri, 10 Dec 2021 21:29:19: 10000000 INFO @ Fri, 10 Dec 2021 21:29:21: 13000000 INFO @ Fri, 10 Dec 2021 21:29:21: 6000000 INFO @ Fri, 10 Dec 2021 21:29:26: 11000000 INFO @ Fri, 10 Dec 2021 21:29:29: 7000000 INFO @ Fri, 10 Dec 2021 21:29:29: 14000000 INFO @ Fri, 10 Dec 2021 21:29:33: 12000000 INFO @ Fri, 10 Dec 2021 21:29:36: 8000000 INFO @ Fri, 10 Dec 2021 21:29:37: 15000000 INFO @ Fri, 10 Dec 2021 21:29:40: 13000000 INFO @ Fri, 10 Dec 2021 21:29:43: 9000000 INFO @ Fri, 10 Dec 2021 21:29:45: 16000000 INFO @ Fri, 10 Dec 2021 21:29:47: 14000000 INFO @ Fri, 10 Dec 2021 21:29:50: 10000000 INFO @ Fri, 10 Dec 2021 21:29:53: 17000000 INFO @ Fri, 10 Dec 2021 21:29:53: 15000000 INFO @ Fri, 10 Dec 2021 21:29:56: 11000000 INFO @ Fri, 10 Dec 2021 21:30:00: 16000000 INFO @ Fri, 10 Dec 2021 21:30:01: 18000000 INFO @ Fri, 10 Dec 2021 21:30:03: 12000000 INFO @ Fri, 10 Dec 2021 21:30:07: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:30:09: 19000000 INFO @ Fri, 10 Dec 2021 21:30:10: 13000000 INFO @ Fri, 10 Dec 2021 21:30:14: 18000000 INFO @ Fri, 10 Dec 2021 21:30:16: 14000000 INFO @ Fri, 10 Dec 2021 21:30:17: 20000000 INFO @ Fri, 10 Dec 2021 21:30:19: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:30:19: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:30:19: #1 total tags in treatment: 6123522 INFO @ Fri, 10 Dec 2021 21:30:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:30:19: #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 21:30:19: #1 tags after filtering in treatment: 4092962 INFO @ Fri, 10 Dec 2021 21:30:19: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 10 Dec 2021 21:30:19: #1 finished! INFO @ Fri, 10 Dec 2021 21:30:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:30:20: #2 number of paired peaks: 5289 INFO @ Fri, 10 Dec 2021 21:30:20: start model_add_line... INFO @ Fri, 10 Dec 2021 21:30:20: start X-correlation... INFO @ Fri, 10 Dec 2021 21:30:20: end of X-cor INFO @ Fri, 10 Dec 2021 21:30:20: #2 finished! INFO @ Fri, 10 Dec 2021 21:30:20: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 21:30:20: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 21:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.05_model.r WARNING @ Fri, 10 Dec 2021 21:30:20: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:30:20: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 21:30:20: #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 21:30:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:30:21: 19000000 INFO @ Fri, 10 Dec 2021 21:30:23: 15000000 INFO @ Fri, 10 Dec 2021 21:30:28: 20000000 INFO @ Fri, 10 Dec 2021 21:30:29: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:30:29: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:30:29: #1 total tags in treatment: 6123522 INFO @ Fri, 10 Dec 2021 21:30:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:30:29: #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 21:30:30: #1 tags after filtering in treatment: 4092962 INFO @ Fri, 10 Dec 2021 21:30:30: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 10 Dec 2021 21:30:30: #1 finished! INFO @ Fri, 10 Dec 2021 21:30:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:30:30: 16000000 INFO @ Fri, 10 Dec 2021 21:30:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:30:30: #2 number of paired peaks: 5289 INFO @ Fri, 10 Dec 2021 21:30:30: start model_add_line... INFO @ Fri, 10 Dec 2021 21:30:30: start X-correlation... INFO @ Fri, 10 Dec 2021 21:30:30: end of X-cor INFO @ Fri, 10 Dec 2021 21:30:30: #2 finished! INFO @ Fri, 10 Dec 2021 21:30:30: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 21:30:30: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 21:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.10_model.r WARNING @ Fri, 10 Dec 2021 21:30:30: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:30:30: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 21:30:30: #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 21:30:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.05_summits.bed INFO @ Fri, 10 Dec 2021 21:30:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9824 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:30:36: 17000000 INFO @ Fri, 10 Dec 2021 21:30:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:30:43: 18000000 INFO @ Fri, 10 Dec 2021 21:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:30:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.10_summits.bed INFO @ Fri, 10 Dec 2021 21:30:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5975 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:30:49: 19000000 INFO @ Fri, 10 Dec 2021 21:30:56: 20000000 INFO @ Fri, 10 Dec 2021 21:30:58: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:30:58: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:30:58: #1 total tags in treatment: 6123522 INFO @ Fri, 10 Dec 2021 21:30:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:30:58: #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 21:30:58: #1 tags after filtering in treatment: 4092962 INFO @ Fri, 10 Dec 2021 21:30:58: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 10 Dec 2021 21:30:58: #1 finished! INFO @ Fri, 10 Dec 2021 21:30:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:30:58: #2 number of paired peaks: 5289 INFO @ Fri, 10 Dec 2021 21:30:58: start model_add_line... INFO @ Fri, 10 Dec 2021 21:30:58: start X-correlation... INFO @ Fri, 10 Dec 2021 21:30:58: end of X-cor INFO @ Fri, 10 Dec 2021 21:30:58: #2 finished! INFO @ Fri, 10 Dec 2021 21:30:58: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 21:30:58: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 21:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.20_model.r WARNING @ Fri, 10 Dec 2021 21:30:58: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:30:58: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 21:30:58: #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 21:30:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:31:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978777/ERX3978777.20_summits.bed INFO @ Fri, 10 Dec 2021 21:31:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2353 records, 4 fields): 4 millis CompletedMACS2peakCalling