Job ID = 12266674 SRX = SRX8174037 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15332263 spots for SRR11607675/SRR11607675.sra Written 15332263 spots for SRR11607675/SRR11607675.sra Read 7500541 spots for SRR11607694/SRR11607694.sra Written 7500541 spots for SRR11607694/SRR11607694.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267196 ("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: 00:36:17 22832804 reads; of these: 22832804 (100.00%) were paired; of these: 2164570 (9.48%) aligned concordantly 0 times 9439210 (41.34%) aligned concordantly exactly 1 time 11229024 (49.18%) aligned concordantly >1 times ---- 2164570 pairs aligned concordantly 0 times; of these: 677952 (31.32%) aligned discordantly 1 time ---- 1486618 pairs aligned 0 times concordantly or discordantly; of these: 2973236 mates make up the pairs; of these: 1628533 (54.77%) aligned 0 times 404345 (13.60%) aligned exactly 1 time 940358 (31.63%) aligned >1 times 96.43% overall alignment rate Time searching: 00:36:17 Overall time: 00:36:17 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] 7398781 / 21133698 = 0.3501 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:53:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.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 @ Sat, 03 Apr 2021 09:53:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:53:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:53:50: 1000000 INFO @ Sat, 03 Apr 2021 09:53:55: 2000000 INFO @ Sat, 03 Apr 2021 09:54:00: 3000000 INFO @ Sat, 03 Apr 2021 09:54:05: 4000000 INFO @ Sat, 03 Apr 2021 09:54:09: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:54:14: 6000000 INFO @ Sat, 03 Apr 2021 09:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.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 @ Sat, 03 Apr 2021 09:54:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:54:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:54:19: 7000000 INFO @ Sat, 03 Apr 2021 09:54:21: 1000000 INFO @ Sat, 03 Apr 2021 09:54:24: 8000000 INFO @ Sat, 03 Apr 2021 09:54:27: 2000000 INFO @ Sat, 03 Apr 2021 09:54:29: 9000000 INFO @ Sat, 03 Apr 2021 09:54:32: 3000000 INFO @ Sat, 03 Apr 2021 09:54:33: 10000000 INFO @ Sat, 03 Apr 2021 09:54:37: 4000000 INFO @ Sat, 03 Apr 2021 09:54:38: 11000000 INFO @ Sat, 03 Apr 2021 09:54:42: 5000000 INFO @ Sat, 03 Apr 2021 09:54:43: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.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 @ Sat, 03 Apr 2021 09:54:46: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:54:46: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:54:46: 6000000 INFO @ Sat, 03 Apr 2021 09:54:48: 13000000 INFO @ Sat, 03 Apr 2021 09:54:51: 1000000 INFO @ Sat, 03 Apr 2021 09:54:52: 7000000 INFO @ Sat, 03 Apr 2021 09:54:53: 14000000 INFO @ Sat, 03 Apr 2021 09:54:56: 2000000 INFO @ Sat, 03 Apr 2021 09:54:57: 8000000 INFO @ Sat, 03 Apr 2021 09:54:58: 15000000 INFO @ Sat, 03 Apr 2021 09:55:01: 9000000 INFO @ Sat, 03 Apr 2021 09:55:01: 3000000 INFO @ Sat, 03 Apr 2021 09:55:03: 16000000 INFO @ Sat, 03 Apr 2021 09:55:06: 10000000 INFO @ Sat, 03 Apr 2021 09:55:07: 4000000 INFO @ Sat, 03 Apr 2021 09:55:09: 17000000 INFO @ Sat, 03 Apr 2021 09:55:11: 11000000 INFO @ Sat, 03 Apr 2021 09:55:12: 5000000 INFO @ Sat, 03 Apr 2021 09:55:14: 18000000 INFO @ Sat, 03 Apr 2021 09:55:16: 12000000 INFO @ Sat, 03 Apr 2021 09:55:17: 6000000 INFO @ Sat, 03 Apr 2021 09:55:19: 19000000 INFO @ Sat, 03 Apr 2021 09:55:21: 13000000 INFO @ Sat, 03 Apr 2021 09:55:22: 7000000 INFO @ Sat, 03 Apr 2021 09:55:24: 20000000 INFO @ Sat, 03 Apr 2021 09:55:26: 14000000 INFO @ Sat, 03 Apr 2021 09:55:27: 8000000 INFO @ Sat, 03 Apr 2021 09:55:29: 21000000 INFO @ Sat, 03 Apr 2021 09:55:30: 15000000 INFO @ Sat, 03 Apr 2021 09:55:32: 9000000 INFO @ Sat, 03 Apr 2021 09:55:34: 22000000 INFO @ Sat, 03 Apr 2021 09:55:35: 16000000 INFO @ Sat, 03 Apr 2021 09:55:37: 10000000 INFO @ Sat, 03 Apr 2021 09:55:39: 23000000 INFO @ Sat, 03 Apr 2021 09:55:41: 17000000 INFO @ Sat, 03 Apr 2021 09:55:42: 11000000 INFO @ Sat, 03 Apr 2021 09:55:44: 24000000 INFO @ Sat, 03 Apr 2021 09:55:45: 18000000 INFO @ Sat, 03 Apr 2021 09:55:48: 12000000 INFO @ Sat, 03 Apr 2021 09:55:49: 25000000 INFO @ Sat, 03 Apr 2021 09:55:50: 19000000 INFO @ Sat, 03 Apr 2021 09:55:53: 13000000 INFO @ Sat, 03 Apr 2021 09:55:54: 26000000 INFO @ Sat, 03 Apr 2021 09:55:55: 20000000 INFO @ Sat, 03 Apr 2021 09:55:58: 14000000 INFO @ Sat, 03 Apr 2021 09:55:59: 21000000 INFO @ Sat, 03 Apr 2021 09:55:59: 27000000 INFO @ Sat, 03 Apr 2021 09:56:03: 15000000 INFO @ Sat, 03 Apr 2021 09:56:04: 22000000 INFO @ Sat, 03 Apr 2021 09:56:04: 28000000 INFO @ Sat, 03 Apr 2021 09:56:08: 16000000 INFO @ Sat, 03 Apr 2021 09:56:08: 23000000 INFO @ Sat, 03 Apr 2021 09:56:09: 29000000 INFO @ Sat, 03 Apr 2021 09:56:11: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 09:56:11: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 09:56:11: #1 total tags in treatment: 13301749 INFO @ Sat, 03 Apr 2021 09:56:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:56:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:56:11: #1 tags after filtering in treatment: 10577894 INFO @ Sat, 03 Apr 2021 09:56:11: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 09:56:11: #1 finished! INFO @ Sat, 03 Apr 2021 09:56:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:56:12: #2 number of paired peaks: 401 WARNING @ Sat, 03 Apr 2021 09:56:12: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sat, 03 Apr 2021 09:56:12: start model_add_line... INFO @ Sat, 03 Apr 2021 09:56:12: start X-correlation... INFO @ Sat, 03 Apr 2021 09:56:12: end of X-cor INFO @ Sat, 03 Apr 2021 09:56:12: #2 finished! INFO @ Sat, 03 Apr 2021 09:56:12: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Apr 2021 09:56:12: #2 alternative fragment length(s) may be 4,61,585 bps INFO @ Sat, 03 Apr 2021 09:56:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.05_model.r WARNING @ Sat, 03 Apr 2021 09:56:12: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:56:12: #2 You may need to consider one of the other alternative d(s): 4,61,585 WARNING @ Sat, 03 Apr 2021 09:56:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:56:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:56:12: 17000000 INFO @ Sat, 03 Apr 2021 09:56:13: 24000000 INFO @ Sat, 03 Apr 2021 09:56:17: 18000000 INFO @ Sat, 03 Apr 2021 09:56:18: 25000000 INFO @ Sat, 03 Apr 2021 09:56:22: 19000000 INFO @ Sat, 03 Apr 2021 09:56:22: 26000000 INFO @ Sat, 03 Apr 2021 09:56:26: 20000000 INFO @ Sat, 03 Apr 2021 09:56:27: 27000000 INFO @ Sat, 03 Apr 2021 09:56:30: 21000000 INFO @ Sat, 03 Apr 2021 09:56:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:56:32: 28000000 INFO @ Sat, 03 Apr 2021 09:56:35: 22000000 INFO @ Sat, 03 Apr 2021 09:56:37: 29000000 INFO @ Sat, 03 Apr 2021 09:56:38: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 09:56:38: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 09:56:38: #1 total tags in treatment: 13301749 INFO @ Sat, 03 Apr 2021 09:56:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:56:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:56:38: #1 tags after filtering in treatment: 10577894 INFO @ Sat, 03 Apr 2021 09:56:38: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 09:56:38: #1 finished! INFO @ Sat, 03 Apr 2021 09:56:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:56:39: 23000000 INFO @ Sat, 03 Apr 2021 09:56:39: #2 number of paired peaks: 401 WARNING @ Sat, 03 Apr 2021 09:56:39: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sat, 03 Apr 2021 09:56:39: start model_add_line... INFO @ Sat, 03 Apr 2021 09:56:39: start X-correlation... INFO @ Sat, 03 Apr 2021 09:56:39: end of X-cor INFO @ Sat, 03 Apr 2021 09:56:39: #2 finished! INFO @ Sat, 03 Apr 2021 09:56:39: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Apr 2021 09:56:39: #2 alternative fragment length(s) may be 4,61,585 bps INFO @ Sat, 03 Apr 2021 09:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.10_model.r WARNING @ Sat, 03 Apr 2021 09:56:39: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:56:39: #2 You may need to consider one of the other alternative d(s): 4,61,585 WARNING @ Sat, 03 Apr 2021 09:56:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:56:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.05_summits.bed INFO @ Sat, 03 Apr 2021 09:56:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4034 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:56:43: 24000000 INFO @ Sat, 03 Apr 2021 09:56:48: 25000000 INFO @ Sat, 03 Apr 2021 09:56:52: 26000000 INFO @ Sat, 03 Apr 2021 09:56:56: 27000000 INFO @ Sat, 03 Apr 2021 09:56:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:57:00: 28000000 INFO @ Sat, 03 Apr 2021 09:57:05: 29000000 INFO @ Sat, 03 Apr 2021 09:57:06: #1 tag size is determined as 40 bps INFO @ Sat, 03 Apr 2021 09:57:06: #1 tag size = 40 INFO @ Sat, 03 Apr 2021 09:57:06: #1 total tags in treatment: 13301749 INFO @ Sat, 03 Apr 2021 09:57:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:57:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:57:06: #1 tags after filtering in treatment: 10577894 INFO @ Sat, 03 Apr 2021 09:57:06: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 09:57:06: #1 finished! INFO @ Sat, 03 Apr 2021 09:57:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:57:07: #2 number of paired peaks: 401 WARNING @ Sat, 03 Apr 2021 09:57:07: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sat, 03 Apr 2021 09:57:07: start model_add_line... INFO @ Sat, 03 Apr 2021 09:57:07: start X-correlation... INFO @ Sat, 03 Apr 2021 09:57:07: end of X-cor INFO @ Sat, 03 Apr 2021 09:57:07: #2 finished! INFO @ Sat, 03 Apr 2021 09:57:07: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Apr 2021 09:57:07: #2 alternative fragment length(s) may be 4,61,585 bps INFO @ Sat, 03 Apr 2021 09:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.20_model.r WARNING @ Sat, 03 Apr 2021 09:57:07: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:57:07: #2 You may need to consider one of the other alternative d(s): 4,61,585 WARNING @ Sat, 03 Apr 2021 09:57:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:57:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.10_summits.bed INFO @ Sat, 03 Apr 2021 09:57:10: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1261 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:57:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:57:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:57:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:57:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8174037/SRX8174037.20_summits.bed INFO @ Sat, 03 Apr 2021 09:57:37: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (264 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。