Job ID = 12265457 SRX = SRX7192193 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11458213 spots for SRR10503237/SRR10503237.sra Written 11458213 spots for SRR10503237/SRR10503237.sra Read 11151307 spots for SRR10503238/SRR10503238.sra Written 11151307 spots for SRR10503238/SRR10503238.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265716 ("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: 00:36:51 22609520 reads; of these: 22609520 (100.00%) were paired; of these: 3157712 (13.97%) aligned concordantly 0 times 15120466 (66.88%) aligned concordantly exactly 1 time 4331342 (19.16%) aligned concordantly >1 times ---- 3157712 pairs aligned concordantly 0 times; of these: 965680 (30.58%) aligned discordantly 1 time ---- 2192032 pairs aligned 0 times concordantly or discordantly; of these: 4384064 mates make up the pairs; of these: 3212897 (73.29%) aligned 0 times 721089 (16.45%) aligned exactly 1 time 450078 (10.27%) aligned >1 times 92.89% overall alignment rate Time searching: 00:36:51 Overall time: 00:36:51 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] 3529539 / 20260442 = 0.1742 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 07:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.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 07:59:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:59:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:59:47: 1000000 INFO @ Sat, 03 Apr 2021 07:59:52: 2000000 INFO @ Sat, 03 Apr 2021 07:59:58: 3000000 INFO @ Sat, 03 Apr 2021 08:00:04: 4000000 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 08:00:10: 5000000 INFO @ Sat, 03 Apr 2021 08:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.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 08:00:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:00:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:00:16: 6000000 INFO @ Sat, 03 Apr 2021 08:00:17: 1000000 INFO @ Sat, 03 Apr 2021 08:00:22: 7000000 INFO @ Sat, 03 Apr 2021 08:00:23: 2000000 INFO @ Sat, 03 Apr 2021 08:00:28: 8000000 INFO @ Sat, 03 Apr 2021 08:00:29: 3000000 INFO @ Sat, 03 Apr 2021 08:00:35: 9000000 INFO @ Sat, 03 Apr 2021 08:00:36: 4000000 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 08:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.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 08:00:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:00:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:00:41: 10000000 INFO @ Sat, 03 Apr 2021 08:00:42: 5000000 INFO @ Sat, 03 Apr 2021 08:00:47: 1000000 INFO @ Sat, 03 Apr 2021 08:00:48: 11000000 INFO @ Sat, 03 Apr 2021 08:00:49: 6000000 INFO @ Sat, 03 Apr 2021 08:00:53: 2000000 INFO @ Sat, 03 Apr 2021 08:00:54: 12000000 INFO @ Sat, 03 Apr 2021 08:00:55: 7000000 INFO @ Sat, 03 Apr 2021 08:01:00: 3000000 INFO @ Sat, 03 Apr 2021 08:01:01: 13000000 INFO @ Sat, 03 Apr 2021 08:01:02: 8000000 INFO @ Sat, 03 Apr 2021 08:01:06: 4000000 INFO @ Sat, 03 Apr 2021 08:01:07: 14000000 INFO @ Sat, 03 Apr 2021 08:01:09: 9000000 INFO @ Sat, 03 Apr 2021 08:01:12: 5000000 INFO @ Sat, 03 Apr 2021 08:01:14: 15000000 INFO @ Sat, 03 Apr 2021 08:01:15: 10000000 INFO @ Sat, 03 Apr 2021 08:01:19: 6000000 INFO @ Sat, 03 Apr 2021 08:01:21: 16000000 INFO @ Sat, 03 Apr 2021 08:01:22: 11000000 INFO @ Sat, 03 Apr 2021 08:01:25: 7000000 INFO @ Sat, 03 Apr 2021 08:01:27: 17000000 INFO @ Sat, 03 Apr 2021 08:01:28: 12000000 INFO @ Sat, 03 Apr 2021 08:01:31: 8000000 INFO @ Sat, 03 Apr 2021 08:01:34: 18000000 INFO @ Sat, 03 Apr 2021 08:01:35: 13000000 INFO @ Sat, 03 Apr 2021 08:01:38: 9000000 INFO @ Sat, 03 Apr 2021 08:01:40: 19000000 INFO @ Sat, 03 Apr 2021 08:01:42: 14000000 INFO @ Sat, 03 Apr 2021 08:01:45: 10000000 INFO @ Sat, 03 Apr 2021 08:01:47: 20000000 INFO @ Sat, 03 Apr 2021 08:01:49: 15000000 INFO @ Sat, 03 Apr 2021 08:01:51: 11000000 INFO @ Sat, 03 Apr 2021 08:01:53: 21000000 INFO @ Sat, 03 Apr 2021 08:01:55: 16000000 INFO @ Sat, 03 Apr 2021 08:01:58: 12000000 INFO @ Sat, 03 Apr 2021 08:02:00: 22000000 INFO @ Sat, 03 Apr 2021 08:02:02: 17000000 INFO @ Sat, 03 Apr 2021 08:02:04: 13000000 INFO @ Sat, 03 Apr 2021 08:02:07: 23000000 INFO @ Sat, 03 Apr 2021 08:02:08: 18000000 INFO @ Sat, 03 Apr 2021 08:02:11: 14000000 INFO @ Sat, 03 Apr 2021 08:02:14: 24000000 INFO @ Sat, 03 Apr 2021 08:02:15: 19000000 INFO @ Sat, 03 Apr 2021 08:02:18: 15000000 INFO @ Sat, 03 Apr 2021 08:02:20: 25000000 INFO @ Sat, 03 Apr 2021 08:02:22: 20000000 INFO @ Sat, 03 Apr 2021 08:02:24: 16000000 INFO @ Sat, 03 Apr 2021 08:02:27: 26000000 INFO @ Sat, 03 Apr 2021 08:02:28: 21000000 INFO @ Sat, 03 Apr 2021 08:02:30: 17000000 INFO @ Sat, 03 Apr 2021 08:02:33: 27000000 INFO @ Sat, 03 Apr 2021 08:02:35: 22000000 INFO @ Sat, 03 Apr 2021 08:02:36: 18000000 INFO @ Sat, 03 Apr 2021 08:02:40: 28000000 INFO @ Sat, 03 Apr 2021 08:02:41: 23000000 INFO @ Sat, 03 Apr 2021 08:02:42: 19000000 INFO @ Sat, 03 Apr 2021 08:02:46: 29000000 INFO @ Sat, 03 Apr 2021 08:02:48: 24000000 INFO @ Sat, 03 Apr 2021 08:02:48: 20000000 INFO @ Sat, 03 Apr 2021 08:02:53: 30000000 INFO @ Sat, 03 Apr 2021 08:02:54: 25000000 INFO @ Sat, 03 Apr 2021 08:02:55: 21000000 INFO @ Sat, 03 Apr 2021 08:02:59: 31000000 INFO @ Sat, 03 Apr 2021 08:03:01: 22000000 INFO @ Sat, 03 Apr 2021 08:03:01: 26000000 INFO @ Sat, 03 Apr 2021 08:03:05: 32000000 INFO @ Sat, 03 Apr 2021 08:03:07: 23000000 INFO @ Sat, 03 Apr 2021 08:03:08: 27000000 INFO @ Sat, 03 Apr 2021 08:03:12: 33000000 INFO @ Sat, 03 Apr 2021 08:03:13: 24000000 INFO @ Sat, 03 Apr 2021 08:03:14: 28000000 INFO @ Sat, 03 Apr 2021 08:03:18: 34000000 INFO @ Sat, 03 Apr 2021 08:03:19: 25000000 INFO @ Sat, 03 Apr 2021 08:03:21: 29000000 INFO @ Sat, 03 Apr 2021 08:03:24: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 08:03:24: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 08:03:24: #1 total tags in treatment: 16027685 INFO @ Sat, 03 Apr 2021 08:03:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:03:24: #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 08:03:24: #1 tags after filtering in treatment: 12259229 INFO @ Sat, 03 Apr 2021 08:03:24: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:03:24: #1 finished! INFO @ Sat, 03 Apr 2021 08:03:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:03:25: 26000000 INFO @ Sat, 03 Apr 2021 08:03:25: #2 number of paired peaks: 874 WARNING @ Sat, 03 Apr 2021 08:03:25: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 03 Apr 2021 08:03:25: start model_add_line... INFO @ Sat, 03 Apr 2021 08:03:25: start X-correlation... INFO @ Sat, 03 Apr 2021 08:03:26: end of X-cor INFO @ Sat, 03 Apr 2021 08:03:26: #2 finished! INFO @ Sat, 03 Apr 2021 08:03:26: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 08:03:26: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Apr 2021 08:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.05_model.r WARNING @ Sat, 03 Apr 2021 08:03:26: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:03:26: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Apr 2021 08:03:26: #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 08:03:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:03:27: 30000000 INFO @ Sat, 03 Apr 2021 08:03:31: 27000000 INFO @ Sat, 03 Apr 2021 08:03:33: 31000000 INFO @ Sat, 03 Apr 2021 08:03:37: 28000000 INFO @ Sat, 03 Apr 2021 08:03:39: 32000000 INFO @ Sat, 03 Apr 2021 08:03:44: 29000000 INFO @ Sat, 03 Apr 2021 08:03:45: 33000000 INFO @ Sat, 03 Apr 2021 08:03:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:03:50: 30000000 INFO @ Sat, 03 Apr 2021 08:03:51: 34000000 INFO @ Sat, 03 Apr 2021 08:03:56: 31000000 INFO @ Sat, 03 Apr 2021 08:03:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 08:03:57: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 08:03:57: #1 total tags in treatment: 16027685 INFO @ Sat, 03 Apr 2021 08:03:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:03:57: #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 08:03:57: #1 tags after filtering in treatment: 12259229 INFO @ Sat, 03 Apr 2021 08:03:57: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:03:57: #1 finished! INFO @ Sat, 03 Apr 2021 08:03:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:03:58: #2 number of paired peaks: 874 WARNING @ Sat, 03 Apr 2021 08:03:58: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 03 Apr 2021 08:03:58: start model_add_line... INFO @ Sat, 03 Apr 2021 08:03:58: start X-correlation... INFO @ Sat, 03 Apr 2021 08:03:58: end of X-cor INFO @ Sat, 03 Apr 2021 08:03:58: #2 finished! INFO @ Sat, 03 Apr 2021 08:03:58: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 08:03:58: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Apr 2021 08:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.10_model.r WARNING @ Sat, 03 Apr 2021 08:03:58: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:03:58: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Apr 2021 08:03:58: #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 08:03:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:04:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:04:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:04:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.05_summits.bed INFO @ Sat, 03 Apr 2021 08:04:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11667 records, 4 fields): 15 millis INFO @ Sat, 03 Apr 2021 08:04:01: 32000000 CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:04:07: 33000000 INFO @ Sat, 03 Apr 2021 08:04:13: 34000000 INFO @ Sat, 03 Apr 2021 08:04:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 08:04:18: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 08:04:18: #1 total tags in treatment: 16027685 INFO @ Sat, 03 Apr 2021 08:04:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:04:18: #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 08:04:19: #1 tags after filtering in treatment: 12259229 INFO @ Sat, 03 Apr 2021 08:04:19: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:04:19: #1 finished! INFO @ Sat, 03 Apr 2021 08:04:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:04:20: #2 number of paired peaks: 874 WARNING @ Sat, 03 Apr 2021 08:04:20: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Sat, 03 Apr 2021 08:04:20: start model_add_line... INFO @ Sat, 03 Apr 2021 08:04:20: start X-correlation... INFO @ Sat, 03 Apr 2021 08:04:20: end of X-cor INFO @ Sat, 03 Apr 2021 08:04:20: #2 finished! INFO @ Sat, 03 Apr 2021 08:04:20: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 08:04:20: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Apr 2021 08:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.20_model.r WARNING @ Sat, 03 Apr 2021 08:04:20: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:04:20: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Apr 2021 08:04:20: #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 08:04:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:04:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.10_summits.bed INFO @ Sat, 03 Apr 2021 08:04:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6544 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:04:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192193/SRX7192193.20_summits.bed INFO @ Sat, 03 Apr 2021 08:04:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2397 records, 4 fields): 5 millis CompletedMACS2peakCalling