Job ID = 14168257 SRX = ERX3978728 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19484328 spots for ERR3975737/ERR3975737.sra Written 19484328 spots for ERR3975737/ERR3975737.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169294 ("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: 00:34:40 19484328 reads; of these: 19484328 (100.00%) were paired; of these: 8224836 (42.21%) aligned concordantly 0 times 6804015 (34.92%) aligned concordantly exactly 1 time 4455477 (22.87%) aligned concordantly >1 times ---- 8224836 pairs aligned concordantly 0 times; of these: 1898618 (23.08%) aligned discordantly 1 time ---- 6326218 pairs aligned 0 times concordantly or discordantly; of these: 12652436 mates make up the pairs; of these: 9226777 (72.92%) aligned 0 times 383850 (3.03%) aligned exactly 1 time 3041809 (24.04%) aligned >1 times 76.32% overall alignment rate Time searching: 00:34:40 Overall time: 00:34:40 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 20 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] 3300331 / 13064864 = 0.2526 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 17:22:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.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 17:22:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:22:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:22:24: 1000000 INFO @ Fri, 10 Dec 2021 17:22:30: 2000000 INFO @ Fri, 10 Dec 2021 17:22:35: 3000000 INFO @ Fri, 10 Dec 2021 17:22:41: 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 17:22:47: 5000000 INFO @ Fri, 10 Dec 2021 17:22:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.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 17:22:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:22:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:22:52: 6000000 INFO @ Fri, 10 Dec 2021 17:22:54: 1000000 INFO @ Fri, 10 Dec 2021 17:22:58: 7000000 INFO @ Fri, 10 Dec 2021 17:23:00: 2000000 INFO @ Fri, 10 Dec 2021 17:23:04: 8000000 INFO @ Fri, 10 Dec 2021 17:23:05: 3000000 INFO @ Fri, 10 Dec 2021 17:23:10: 9000000 INFO @ Fri, 10 Dec 2021 17:23:11: 4000000 INFO @ Fri, 10 Dec 2021 17:23:16: 10000000 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 17:23:17: 5000000 INFO @ Fri, 10 Dec 2021 17:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.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 17:23:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:23:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:23:22: 11000000 INFO @ Fri, 10 Dec 2021 17:23:23: 6000000 INFO @ Fri, 10 Dec 2021 17:23:24: 1000000 INFO @ Fri, 10 Dec 2021 17:23:27: 12000000 INFO @ Fri, 10 Dec 2021 17:23:29: 7000000 INFO @ Fri, 10 Dec 2021 17:23:30: 2000000 INFO @ Fri, 10 Dec 2021 17:23:33: 13000000 INFO @ Fri, 10 Dec 2021 17:23:35: 8000000 INFO @ Fri, 10 Dec 2021 17:23:35: 3000000 INFO @ Fri, 10 Dec 2021 17:23:39: 14000000 INFO @ Fri, 10 Dec 2021 17:23:41: 9000000 INFO @ Fri, 10 Dec 2021 17:23:41: 4000000 INFO @ Fri, 10 Dec 2021 17:23:45: 15000000 INFO @ Fri, 10 Dec 2021 17:23:46: 10000000 INFO @ Fri, 10 Dec 2021 17:23:47: 5000000 INFO @ Fri, 10 Dec 2021 17:23:50: 16000000 INFO @ Fri, 10 Dec 2021 17:23:52: 11000000 INFO @ Fri, 10 Dec 2021 17:23:53: 6000000 INFO @ Fri, 10 Dec 2021 17:23:55: 17000000 INFO @ Fri, 10 Dec 2021 17:23:58: 12000000 INFO @ Fri, 10 Dec 2021 17:23:59: 7000000 INFO @ Fri, 10 Dec 2021 17:24:01: 18000000 INFO @ Fri, 10 Dec 2021 17:24:04: 13000000 INFO @ Fri, 10 Dec 2021 17:24:05: 8000000 INFO @ Fri, 10 Dec 2021 17:24:06: 19000000 INFO @ Fri, 10 Dec 2021 17:24:10: 14000000 INFO @ Fri, 10 Dec 2021 17:24:11: 9000000 INFO @ Fri, 10 Dec 2021 17:24:12: 20000000 INFO @ Fri, 10 Dec 2021 17:24:15: 15000000 INFO @ Fri, 10 Dec 2021 17:24:16: 10000000 INFO @ Fri, 10 Dec 2021 17:24:18: 21000000 INFO @ Fri, 10 Dec 2021 17:24:21: 16000000 INFO @ Fri, 10 Dec 2021 17:24:22: 11000000 INFO @ Fri, 10 Dec 2021 17:24:24: 22000000 INFO @ Fri, 10 Dec 2021 17:24:26: 17000000 INFO @ Fri, 10 Dec 2021 17:24:28: 12000000 INFO @ Fri, 10 Dec 2021 17:24:30: 23000000 INFO @ Fri, 10 Dec 2021 17:24:31: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 17:24:31: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 17:24:31: #1 total tags in treatment: 8081187 INFO @ Fri, 10 Dec 2021 17:24:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:24:31: #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 17:24:31: #1 tags after filtering in treatment: 6229944 INFO @ Fri, 10 Dec 2021 17:24:31: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Dec 2021 17:24:31: #1 finished! INFO @ Fri, 10 Dec 2021 17:24:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:24:31: #2 number of paired peaks: 2808 INFO @ Fri, 10 Dec 2021 17:24:31: start model_add_line... INFO @ Fri, 10 Dec 2021 17:24:31: start X-correlation... INFO @ Fri, 10 Dec 2021 17:24:31: end of X-cor INFO @ Fri, 10 Dec 2021 17:24:31: #2 finished! INFO @ Fri, 10 Dec 2021 17:24:31: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Dec 2021 17:24:31: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Dec 2021 17:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.05_model.r WARNING @ Fri, 10 Dec 2021 17:24:31: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:24:31: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 10 Dec 2021 17:24:31: #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 17:24:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:24:32: 18000000 INFO @ Fri, 10 Dec 2021 17:24:34: 13000000 INFO @ Fri, 10 Dec 2021 17:24:37: 19000000 INFO @ Fri, 10 Dec 2021 17:24:40: 14000000 INFO @ Fri, 10 Dec 2021 17:24:43: 20000000 INFO @ Fri, 10 Dec 2021 17:24:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:24:45: 15000000 INFO @ Fri, 10 Dec 2021 17:24:49: 21000000 INFO @ Fri, 10 Dec 2021 17:24:50: 16000000 INFO @ Fri, 10 Dec 2021 17:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.05_summits.bed INFO @ Fri, 10 Dec 2021 17:24:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10050 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:24:54: 22000000 INFO @ Fri, 10 Dec 2021 17:24:56: 17000000 INFO @ Fri, 10 Dec 2021 17:25:00: 23000000 INFO @ Fri, 10 Dec 2021 17:25:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 17:25:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 17:25:01: #1 total tags in treatment: 8081187 INFO @ Fri, 10 Dec 2021 17:25:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:25:01: #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 17:25:01: 18000000 INFO @ Fri, 10 Dec 2021 17:25:01: #1 tags after filtering in treatment: 6229944 INFO @ Fri, 10 Dec 2021 17:25:01: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Dec 2021 17:25:01: #1 finished! INFO @ Fri, 10 Dec 2021 17:25:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:25:02: #2 number of paired peaks: 2808 INFO @ Fri, 10 Dec 2021 17:25:02: start model_add_line... INFO @ Fri, 10 Dec 2021 17:25:02: start X-correlation... INFO @ Fri, 10 Dec 2021 17:25:02: end of X-cor INFO @ Fri, 10 Dec 2021 17:25:02: #2 finished! INFO @ Fri, 10 Dec 2021 17:25:02: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Dec 2021 17:25:02: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Dec 2021 17:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.10_model.r WARNING @ Fri, 10 Dec 2021 17:25:02: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:25:02: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 10 Dec 2021 17:25:02: #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 17:25:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:25:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:25:12: 20000000 INFO @ Fri, 10 Dec 2021 17:25:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:25:18: 21000000 INFO @ Fri, 10 Dec 2021 17:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.10_summits.bed INFO @ Fri, 10 Dec 2021 17:25:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5391 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:25:24: 22000000 INFO @ Fri, 10 Dec 2021 17:25:29: 23000000 INFO @ Fri, 10 Dec 2021 17:25:30: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 17:25:30: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 17:25:30: #1 total tags in treatment: 8081187 INFO @ Fri, 10 Dec 2021 17:25:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:25:30: #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 17:25:30: #1 tags after filtering in treatment: 6229944 INFO @ Fri, 10 Dec 2021 17:25:30: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 10 Dec 2021 17:25:30: #1 finished! INFO @ Fri, 10 Dec 2021 17:25:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:25:31: #2 number of paired peaks: 2808 INFO @ Fri, 10 Dec 2021 17:25:31: start model_add_line... INFO @ Fri, 10 Dec 2021 17:25:31: start X-correlation... INFO @ Fri, 10 Dec 2021 17:25:31: end of X-cor INFO @ Fri, 10 Dec 2021 17:25:31: #2 finished! INFO @ Fri, 10 Dec 2021 17:25:31: #2 predicted fragment length is 189 bps INFO @ Fri, 10 Dec 2021 17:25:31: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 10 Dec 2021 17:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.20_model.r WARNING @ Fri, 10 Dec 2021 17:25:31: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:25:31: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 10 Dec 2021 17:25:31: #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 17:25:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:25:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:25:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978728/ERX3978728.20_summits.bed INFO @ Fri, 10 Dec 2021 17:25:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1926 records, 4 fields): 3 millis CompletedMACS2peakCalling