Job ID = 14168520 SRX = ERX3978753 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16538930 spots for ERR3975765/ERR3975765.sra Written 16538930 spots for ERR3975765/ERR3975765.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169692 ("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: 00:27:52 16538930 reads; of these: 16538930 (100.00%) were paired; of these: 7304189 (44.16%) aligned concordantly 0 times 4198569 (25.39%) aligned concordantly exactly 1 time 5036172 (30.45%) aligned concordantly >1 times ---- 7304189 pairs aligned concordantly 0 times; of these: 1101283 (15.08%) aligned discordantly 1 time ---- 6202906 pairs aligned 0 times concordantly or discordantly; of these: 12405812 mates make up the pairs; of these: 8227436 (66.32%) aligned 0 times 282169 (2.27%) aligned exactly 1 time 3896207 (31.41%) aligned >1 times 75.13% overall alignment rate Time searching: 00:27:52 Overall time: 00:27:52 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] 3776503 / 10236327 = 0.3689 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 19:26:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.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 19:26:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:26:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:26:53: 1000000 INFO @ Fri, 10 Dec 2021 19:27:01: 2000000 INFO @ Fri, 10 Dec 2021 19:27:08: 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 19:27:15: 4000000 INFO @ Fri, 10 Dec 2021 19:27:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.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 19:27:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:27:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:27:22: 5000000 INFO @ Fri, 10 Dec 2021 19:27:23: 1000000 INFO @ Fri, 10 Dec 2021 19:27:30: 6000000 INFO @ Fri, 10 Dec 2021 19:27:30: 2000000 INFO @ Fri, 10 Dec 2021 19:27:37: 3000000 INFO @ Fri, 10 Dec 2021 19:27:37: 7000000 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 19:27:45: 4000000 INFO @ Fri, 10 Dec 2021 19:27:45: 8000000 INFO @ Fri, 10 Dec 2021 19:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.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 19:27:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:27:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:27:52: 5000000 INFO @ Fri, 10 Dec 2021 19:27:52: 9000000 INFO @ Fri, 10 Dec 2021 19:27:54: 1000000 INFO @ Fri, 10 Dec 2021 19:28:00: 6000000 INFO @ Fri, 10 Dec 2021 19:28:00: 10000000 INFO @ Fri, 10 Dec 2021 19:28:02: 2000000 INFO @ Fri, 10 Dec 2021 19:28:07: 11000000 INFO @ Fri, 10 Dec 2021 19:28:07: 7000000 INFO @ Fri, 10 Dec 2021 19:28:11: 3000000 INFO @ Fri, 10 Dec 2021 19:28:14: 12000000 INFO @ Fri, 10 Dec 2021 19:28:14: 8000000 INFO @ Fri, 10 Dec 2021 19:28:20: 4000000 INFO @ Fri, 10 Dec 2021 19:28:21: 13000000 INFO @ Fri, 10 Dec 2021 19:28:22: 9000000 INFO @ Fri, 10 Dec 2021 19:28:28: 14000000 INFO @ Fri, 10 Dec 2021 19:28:29: 10000000 INFO @ Fri, 10 Dec 2021 19:28:29: 5000000 INFO @ Fri, 10 Dec 2021 19:28:36: 15000000 INFO @ Fri, 10 Dec 2021 19:28:36: 11000000 INFO @ Fri, 10 Dec 2021 19:28:38: 6000000 INFO @ Fri, 10 Dec 2021 19:28:44: 12000000 INFO @ Fri, 10 Dec 2021 19:28:44: 16000000 INFO @ Fri, 10 Dec 2021 19:28:47: 7000000 INFO @ Fri, 10 Dec 2021 19:28:51: 13000000 INFO @ Fri, 10 Dec 2021 19:28:51: 17000000 INFO @ Fri, 10 Dec 2021 19:28:53: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:28:53: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:28:53: #1 total tags in treatment: 5546935 INFO @ Fri, 10 Dec 2021 19:28:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:28:53: #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 19:28:54: #1 tags after filtering in treatment: 4114009 INFO @ Fri, 10 Dec 2021 19:28:54: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:28:54: #1 finished! INFO @ Fri, 10 Dec 2021 19:28:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:28:54: #2 number of paired peaks: 4033 INFO @ Fri, 10 Dec 2021 19:28:54: start model_add_line... INFO @ Fri, 10 Dec 2021 19:28:54: start X-correlation... INFO @ Fri, 10 Dec 2021 19:28:54: end of X-cor INFO @ Fri, 10 Dec 2021 19:28:54: #2 finished! INFO @ Fri, 10 Dec 2021 19:28:54: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 19:28:54: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 19:28:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.05_model.r WARNING @ Fri, 10 Dec 2021 19:28:54: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:28:54: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 19:28:54: #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 19:28:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:28:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:28:56: 8000000 INFO @ Fri, 10 Dec 2021 19:28:58: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:29:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:29:05: 15000000 INFO @ Fri, 10 Dec 2021 19:29:05: 9000000 INFO @ Fri, 10 Dec 2021 19:29:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:29:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:29:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.05_summits.bed INFO @ Fri, 10 Dec 2021 19:29:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9629 records, 4 fields): 87 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:29:12: 16000000 INFO @ Fri, 10 Dec 2021 19:29:13: 10000000 INFO @ Fri, 10 Dec 2021 19:29:20: 17000000 INFO @ Fri, 10 Dec 2021 19:29:22: 11000000 INFO @ Fri, 10 Dec 2021 19:29:22: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:29:22: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:29:22: #1 total tags in treatment: 5546935 INFO @ Fri, 10 Dec 2021 19:29:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:29:22: #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 19:29:22: #1 tags after filtering in treatment: 4114009 INFO @ Fri, 10 Dec 2021 19:29:22: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:29:22: #1 finished! INFO @ Fri, 10 Dec 2021 19:29:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:29:22: #2 number of paired peaks: 4033 INFO @ Fri, 10 Dec 2021 19:29:22: start model_add_line... INFO @ Fri, 10 Dec 2021 19:29:22: start X-correlation... INFO @ Fri, 10 Dec 2021 19:29:22: end of X-cor INFO @ Fri, 10 Dec 2021 19:29:22: #2 finished! INFO @ Fri, 10 Dec 2021 19:29:22: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 19:29:22: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 19:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.10_model.r WARNING @ Fri, 10 Dec 2021 19:29:22: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:29:22: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 19:29:22: #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 19:29:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:29:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:29:29: 12000000 INFO @ Fri, 10 Dec 2021 19:29:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.10_summits.bed INFO @ Fri, 10 Dec 2021 19:29:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4988 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:29:37: 13000000 INFO @ Fri, 10 Dec 2021 19:29:45: 14000000 INFO @ Fri, 10 Dec 2021 19:29:53: 15000000 INFO @ Fri, 10 Dec 2021 19:30:01: 16000000 INFO @ Fri, 10 Dec 2021 19:30:09: 17000000 INFO @ Fri, 10 Dec 2021 19:30:11: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:30:11: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:30:11: #1 total tags in treatment: 5546935 INFO @ Fri, 10 Dec 2021 19:30:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:30:11: #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 19:30:11: #1 tags after filtering in treatment: 4114009 INFO @ Fri, 10 Dec 2021 19:30:11: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:30:11: #1 finished! INFO @ Fri, 10 Dec 2021 19:30:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:30:12: #2 number of paired peaks: 4033 INFO @ Fri, 10 Dec 2021 19:30:12: start model_add_line... INFO @ Fri, 10 Dec 2021 19:30:12: start X-correlation... INFO @ Fri, 10 Dec 2021 19:30:12: end of X-cor INFO @ Fri, 10 Dec 2021 19:30:12: #2 finished! INFO @ Fri, 10 Dec 2021 19:30:12: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 19:30:12: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 19:30:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.20_model.r WARNING @ Fri, 10 Dec 2021 19:30:12: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:30:12: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 19:30:12: #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 19:30:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:30:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978753/ERX3978753.20_summits.bed INFO @ Fri, 10 Dec 2021 19:30:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1610 records, 4 fields): 3 millis CompletedMACS2peakCalling