Job ID = 14168182 SRX = ERX3978832 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36690236 spots for ERR3975901/ERR3975901.sra Written 36690236 spots for ERR3975901/ERR3975901.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169484 ("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: 01:55:07 36690236 reads; of these: 36690236 (100.00%) were paired; of these: 12749223 (34.75%) aligned concordantly 0 times 18715634 (51.01%) aligned concordantly exactly 1 time 5225379 (14.24%) aligned concordantly >1 times ---- 12749223 pairs aligned concordantly 0 times; of these: 1022751 (8.02%) aligned discordantly 1 time ---- 11726472 pairs aligned 0 times concordantly or discordantly; of these: 23452944 mates make up the pairs; of these: 11852459 (50.54%) aligned 0 times 7079606 (30.19%) aligned exactly 1 time 4520879 (19.28%) aligned >1 times 83.85% overall alignment rate Time searching: 01:55:07 Overall time: 01:55:07 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 28 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] 18446045 / 24591466 = 0.7501 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 18:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.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 18:10:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:29: 1000000 INFO @ Fri, 10 Dec 2021 18:10:35: 2000000 INFO @ Fri, 10 Dec 2021 18:10:40: 3000000 INFO @ Fri, 10 Dec 2021 18:10:45: 4000000 INFO @ Fri, 10 Dec 2021 18:10:51: 5000000 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 18:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.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 18:10:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:10:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:10:57: 6000000 INFO @ Fri, 10 Dec 2021 18:11:00: 1000000 INFO @ Fri, 10 Dec 2021 18:11:04: 7000000 INFO @ Fri, 10 Dec 2021 18:11:07: 2000000 INFO @ Fri, 10 Dec 2021 18:11:10: 8000000 INFO @ Fri, 10 Dec 2021 18:11:14: 3000000 INFO @ Fri, 10 Dec 2021 18:11:17: 9000000 INFO @ Fri, 10 Dec 2021 18:11:20: 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 18:11:23: 10000000 INFO @ Fri, 10 Dec 2021 18:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.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 18:11:24: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:11:24: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:11:27: 5000000 INFO @ Fri, 10 Dec 2021 18:11:30: 11000000 INFO @ Fri, 10 Dec 2021 18:11:31: 1000000 INFO @ Fri, 10 Dec 2021 18:11:34: 6000000 INFO @ Fri, 10 Dec 2021 18:11:37: 12000000 INFO @ Fri, 10 Dec 2021 18:11:38: 2000000 INFO @ Fri, 10 Dec 2021 18:11:41: 7000000 INFO @ Fri, 10 Dec 2021 18:11:44: 13000000 INFO @ Fri, 10 Dec 2021 18:11:46: 3000000 INFO @ Fri, 10 Dec 2021 18:11:48: 8000000 INFO @ Fri, 10 Dec 2021 18:11:51: 14000000 INFO @ Fri, 10 Dec 2021 18:11:53: 4000000 INFO @ Fri, 10 Dec 2021 18:11:55: 9000000 INFO @ Fri, 10 Dec 2021 18:11:58: 15000000 INFO @ Fri, 10 Dec 2021 18:12:01: 5000000 INFO @ Fri, 10 Dec 2021 18:12:02: 10000000 INFO @ Fri, 10 Dec 2021 18:12:05: 16000000 INFO @ Fri, 10 Dec 2021 18:12:08: 6000000 INFO @ Fri, 10 Dec 2021 18:12:09: 11000000 INFO @ Fri, 10 Dec 2021 18:12:12: 17000000 INFO @ Fri, 10 Dec 2021 18:12:16: 7000000 INFO @ Fri, 10 Dec 2021 18:12:16: 12000000 INFO @ Fri, 10 Dec 2021 18:12:20: 18000000 INFO @ Fri, 10 Dec 2021 18:12:23: 13000000 INFO @ Fri, 10 Dec 2021 18:12:23: 8000000 INFO @ Fri, 10 Dec 2021 18:12:27: 19000000 INFO @ Fri, 10 Dec 2021 18:12:30: 14000000 INFO @ Fri, 10 Dec 2021 18:12:31: 9000000 INFO @ Fri, 10 Dec 2021 18:12:34: 20000000 INFO @ Fri, 10 Dec 2021 18:12:37: 15000000 INFO @ Fri, 10 Dec 2021 18:12:38: 10000000 INFO @ Fri, 10 Dec 2021 18:12:41: 21000000 INFO @ Fri, 10 Dec 2021 18:12:44: 16000000 INFO @ Fri, 10 Dec 2021 18:12:46: 11000000 INFO @ Fri, 10 Dec 2021 18:12:48: 22000000 INFO @ Fri, 10 Dec 2021 18:12:51: 17000000 INFO @ Fri, 10 Dec 2021 18:12:53: 12000000 INFO @ Fri, 10 Dec 2021 18:12:56: 23000000 INFO @ Fri, 10 Dec 2021 18:12:58: 18000000 INFO @ Fri, 10 Dec 2021 18:13:00: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:13:03: 24000000 INFO @ Fri, 10 Dec 2021 18:13:05: 19000000 INFO @ Fri, 10 Dec 2021 18:13:07: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:13:07: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:13:07: #1 total tags in treatment: 6041586 INFO @ Fri, 10 Dec 2021 18:13:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:07: #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 18:13:07: #1 tags after filtering in treatment: 5505920 INFO @ Fri, 10 Dec 2021 18:13:07: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 18:13:07: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:07: #2 number of paired peaks: 857 WARNING @ Fri, 10 Dec 2021 18:13:07: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Fri, 10 Dec 2021 18:13:07: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:08: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:08: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:08: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:08: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 18:13:08: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 18:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.05_model.r WARNING @ Fri, 10 Dec 2021 18:13:08: #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 18:13:08: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 18:13:08: #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 18:13:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:08: 14000000 INFO @ Fri, 10 Dec 2021 18:13:12: 20000000 INFO @ Fri, 10 Dec 2021 18:13:15: 15000000 INFO @ Fri, 10 Dec 2021 18:13:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:13:20: 21000000 INFO @ Fri, 10 Dec 2021 18:13:23: 16000000 INFO @ Fri, 10 Dec 2021 18:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.05_summits.bed INFO @ Fri, 10 Dec 2021 18:13:25: Done! INFO @ Fri, 10 Dec 2021 18:13:27: 22000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5674 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:13:31: 17000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:13:33: 23000000 INFO @ Fri, 10 Dec 2021 18:13:39: 18000000 INFO @ Fri, 10 Dec 2021 18:13:40: 24000000 INFO @ Fri, 10 Dec 2021 18:13:45: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:13:45: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:13:45: #1 total tags in treatment: 6041586 INFO @ Fri, 10 Dec 2021 18:13:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:45: #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 18:13:45: #1 tags after filtering in treatment: 5505920 INFO @ Fri, 10 Dec 2021 18:13:45: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 18:13:45: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:45: #2 number of paired peaks: 857 WARNING @ Fri, 10 Dec 2021 18:13:45: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Fri, 10 Dec 2021 18:13:45: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:45: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:45: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:45: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:45: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 18:13:45: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 18:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.10_model.r WARNING @ Fri, 10 Dec 2021 18:13:45: #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 18:13:45: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 18:13:45: #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 18:13:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:46: 19000000 INFO @ Fri, 10 Dec 2021 18:13:53: 20000000 INFO @ Fri, 10 Dec 2021 18:13:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:01: 21000000 INFO @ Fri, 10 Dec 2021 18:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.10_summits.bed INFO @ Fri, 10 Dec 2021 18:14:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2317 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:14:08: 22000000 INFO @ Fri, 10 Dec 2021 18:14:15: 23000000 INFO @ Fri, 10 Dec 2021 18:14:21: 24000000 INFO @ Fri, 10 Dec 2021 18:14:26: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:14:26: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:14:26: #1 total tags in treatment: 6041586 INFO @ Fri, 10 Dec 2021 18:14:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:14:26: #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 18:14:26: #1 tags after filtering in treatment: 5505920 INFO @ Fri, 10 Dec 2021 18:14:26: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 18:14:26: #1 finished! INFO @ Fri, 10 Dec 2021 18:14:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:14:26: #2 number of paired peaks: 857 WARNING @ Fri, 10 Dec 2021 18:14:26: Fewer paired peaks (857) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 857 pairs to build model! INFO @ Fri, 10 Dec 2021 18:14:26: start model_add_line... INFO @ Fri, 10 Dec 2021 18:14:26: start X-correlation... INFO @ Fri, 10 Dec 2021 18:14:26: end of X-cor INFO @ Fri, 10 Dec 2021 18:14:26: #2 finished! INFO @ Fri, 10 Dec 2021 18:14:26: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 18:14:26: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 18:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.20_model.r WARNING @ Fri, 10 Dec 2021 18:14:26: #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 18:14:26: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 18:14:26: #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 18:14:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:14:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978832/ERX3978832.20_summits.bed INFO @ Fri, 10 Dec 2021 18:14:43: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (766 records, 4 fields): 3 millis CompletedMACS2peakCalling