Job ID = 14168037 SRX = ERX3978933 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26777628 spots for ERR3976003/ERR3976003.sra Written 26777628 spots for ERR3976003/ERR3976003.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169006 ("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: 01:24:34 26777628 reads; of these: 26777628 (100.00%) were paired; of these: 7617214 (28.45%) aligned concordantly 0 times 15215764 (56.82%) aligned concordantly exactly 1 time 3944650 (14.73%) aligned concordantly >1 times ---- 7617214 pairs aligned concordantly 0 times; of these: 832681 (10.93%) aligned discordantly 1 time ---- 6784533 pairs aligned 0 times concordantly or discordantly; of these: 13569066 mates make up the pairs; of these: 6842603 (50.43%) aligned 0 times 4108839 (30.28%) aligned exactly 1 time 2617624 (19.29%) aligned >1 times 87.22% overall alignment rate Time searching: 01:24:34 Overall time: 01:24:34 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] 14816939 / 19687624 = 0.7526 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 16:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.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 16:18:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:18:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:18:32: 1000000 INFO @ Fri, 10 Dec 2021 16:18:38: 2000000 INFO @ Fri, 10 Dec 2021 16:18:44: 3000000 INFO @ Fri, 10 Dec 2021 16:18:50: 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 16:18:56: 5000000 INFO @ Fri, 10 Dec 2021 16:18:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.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 16:18:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:18:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:19:02: 6000000 INFO @ Fri, 10 Dec 2021 16:19:03: 1000000 INFO @ Fri, 10 Dec 2021 16:19:08: 7000000 INFO @ Fri, 10 Dec 2021 16:19:09: 2000000 INFO @ Fri, 10 Dec 2021 16:19:15: 8000000 INFO @ Fri, 10 Dec 2021 16:19:16: 3000000 INFO @ Fri, 10 Dec 2021 16:19:21: 9000000 INFO @ Fri, 10 Dec 2021 16:19:22: 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 16:19:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.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 16:19:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:19:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:19:27: 10000000 INFO @ Fri, 10 Dec 2021 16:19:29: 5000000 INFO @ Fri, 10 Dec 2021 16:19:34: 1000000 INFO @ Fri, 10 Dec 2021 16:19:34: 11000000 INFO @ Fri, 10 Dec 2021 16:19:36: 6000000 INFO @ Fri, 10 Dec 2021 16:19:41: 12000000 INFO @ Fri, 10 Dec 2021 16:19:42: 2000000 INFO @ Fri, 10 Dec 2021 16:19:44: 7000000 INFO @ Fri, 10 Dec 2021 16:19:48: 13000000 INFO @ Fri, 10 Dec 2021 16:19:50: 3000000 INFO @ Fri, 10 Dec 2021 16:19:51: 8000000 INFO @ Fri, 10 Dec 2021 16:19:55: 14000000 INFO @ Fri, 10 Dec 2021 16:19:57: 4000000 INFO @ Fri, 10 Dec 2021 16:19:59: 9000000 INFO @ Fri, 10 Dec 2021 16:20:02: 15000000 INFO @ Fri, 10 Dec 2021 16:20:05: 5000000 INFO @ Fri, 10 Dec 2021 16:20:06: 10000000 INFO @ Fri, 10 Dec 2021 16:20:09: 16000000 INFO @ Fri, 10 Dec 2021 16:20:12: 6000000 INFO @ Fri, 10 Dec 2021 16:20:13: 11000000 INFO @ Fri, 10 Dec 2021 16:20:15: 17000000 INFO @ Fri, 10 Dec 2021 16:20:16: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:20:16: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:20:16: #1 total tags in treatment: 4788352 INFO @ Fri, 10 Dec 2021 16:20:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:20:16: #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 16:20:16: #1 tags after filtering in treatment: 4463143 INFO @ Fri, 10 Dec 2021 16:20:16: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:20:16: #1 finished! INFO @ Fri, 10 Dec 2021 16:20:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:20:16: #2 number of paired peaks: 848 WARNING @ Fri, 10 Dec 2021 16:20:16: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Fri, 10 Dec 2021 16:20:16: start model_add_line... INFO @ Fri, 10 Dec 2021 16:20:16: start X-correlation... INFO @ Fri, 10 Dec 2021 16:20:16: end of X-cor INFO @ Fri, 10 Dec 2021 16:20:16: #2 finished! INFO @ Fri, 10 Dec 2021 16:20:16: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 16:20:16: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 16:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.05_model.r WARNING @ Fri, 10 Dec 2021 16:20:16: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:20:16: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 16:20:16: #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 16:20:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:20:20: 7000000 INFO @ Fri, 10 Dec 2021 16:20:21: 12000000 INFO @ Fri, 10 Dec 2021 16:20:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:20:27: 8000000 INFO @ Fri, 10 Dec 2021 16:20:28: 13000000 INFO @ Fri, 10 Dec 2021 16:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.05_summits.bed INFO @ Fri, 10 Dec 2021 16:20:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4143 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:20:35: 9000000 INFO @ Fri, 10 Dec 2021 16:20:36: 14000000 INFO @ Fri, 10 Dec 2021 16:20:43: 15000000 INFO @ Fri, 10 Dec 2021 16:20:44: 10000000 INFO @ Fri, 10 Dec 2021 16:20:50: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:20:53: 11000000 INFO @ Fri, 10 Dec 2021 16:20:58: 17000000 INFO @ Fri, 10 Dec 2021 16:20:58: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:20:58: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:20:58: #1 total tags in treatment: 4788352 INFO @ Fri, 10 Dec 2021 16:20:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:20:58: #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 16:20:58: #1 tags after filtering in treatment: 4463143 INFO @ Fri, 10 Dec 2021 16:20:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:20:58: #1 finished! INFO @ Fri, 10 Dec 2021 16:20:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:20:59: #2 number of paired peaks: 848 WARNING @ Fri, 10 Dec 2021 16:20:59: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Fri, 10 Dec 2021 16:20:59: start model_add_line... INFO @ Fri, 10 Dec 2021 16:20:59: start X-correlation... INFO @ Fri, 10 Dec 2021 16:20:59: end of X-cor INFO @ Fri, 10 Dec 2021 16:20:59: #2 finished! INFO @ Fri, 10 Dec 2021 16:20:59: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 16:20:59: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 16:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.10_model.r WARNING @ Fri, 10 Dec 2021 16:20:59: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:20:59: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 16:20:59: #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 16:20:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:20:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:21:01: 12000000 INFO @ Fri, 10 Dec 2021 16:21:09: 13000000 INFO @ Fri, 10 Dec 2021 16:21:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.10_summits.bed INFO @ Fri, 10 Dec 2021 16:21:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1401 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:21:17: 14000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:21:25: 15000000 INFO @ Fri, 10 Dec 2021 16:21:32: 16000000 INFO @ Fri, 10 Dec 2021 16:21:40: 17000000 INFO @ Fri, 10 Dec 2021 16:21:41: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 16:21:41: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 16:21:41: #1 total tags in treatment: 4788352 INFO @ Fri, 10 Dec 2021 16:21:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:21:41: #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 16:21:41: #1 tags after filtering in treatment: 4463143 INFO @ Fri, 10 Dec 2021 16:21:41: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 16:21:41: #1 finished! INFO @ Fri, 10 Dec 2021 16:21:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:21:41: #2 number of paired peaks: 848 WARNING @ Fri, 10 Dec 2021 16:21:41: Fewer paired peaks (848) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 848 pairs to build model! INFO @ Fri, 10 Dec 2021 16:21:41: start model_add_line... INFO @ Fri, 10 Dec 2021 16:21:41: start X-correlation... INFO @ Fri, 10 Dec 2021 16:21:41: end of X-cor INFO @ Fri, 10 Dec 2021 16:21:41: #2 finished! INFO @ Fri, 10 Dec 2021 16:21:41: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 16:21:41: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 16:21:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.20_model.r WARNING @ Fri, 10 Dec 2021 16:21:41: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:21:41: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 16:21:41: #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 16:21:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:21:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:21:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978933/ERX3978933.20_summits.bed INFO @ Fri, 10 Dec 2021 16:22:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 2 millis CompletedMACS2peakCalling