Job ID = 14168038 SRX = ERX3978934 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 47187087 spots for ERR3976004/ERR3976004.sra Written 47187087 spots for ERR3976004/ERR3976004.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169132 ("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: 02:06:00 47187087 reads; of these: 47187087 (100.00%) were paired; of these: 7136010 (15.12%) aligned concordantly 0 times 30088565 (63.76%) aligned concordantly exactly 1 time 9962512 (21.11%) aligned concordantly >1 times ---- 7136010 pairs aligned concordantly 0 times; of these: 1166229 (16.34%) aligned discordantly 1 time ---- 5969781 pairs aligned 0 times concordantly or discordantly; of these: 11939562 mates make up the pairs; of these: 7220603 (60.48%) aligned 0 times 2237435 (18.74%) aligned exactly 1 time 2481524 (20.78%) aligned >1 times 92.35% overall alignment rate Time searching: 02:06:00 Overall time: 02:06:00 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 36 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] 26140043 / 41009051 = 0.6374 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 17:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.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 17:11:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:11:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:11:37: 1000000 INFO @ Fri, 10 Dec 2021 17:11:44: 2000000 INFO @ Fri, 10 Dec 2021 17:11:51: 3000000 INFO @ Fri, 10 Dec 2021 17:11:58: 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 17:12:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.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 17:12:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:12:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:12:06: 5000000 INFO @ Fri, 10 Dec 2021 17:12:07: 1000000 INFO @ Fri, 10 Dec 2021 17:12:13: 6000000 INFO @ Fri, 10 Dec 2021 17:12:14: 2000000 INFO @ Fri, 10 Dec 2021 17:12:20: 3000000 INFO @ Fri, 10 Dec 2021 17:12:21: 7000000 INFO @ Fri, 10 Dec 2021 17:12:27: 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 17:12:29: 8000000 INFO @ Fri, 10 Dec 2021 17:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.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 17:12:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:12:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:12:34: 5000000 INFO @ Fri, 10 Dec 2021 17:12:37: 9000000 INFO @ Fri, 10 Dec 2021 17:12:38: 1000000 INFO @ Fri, 10 Dec 2021 17:12:41: 6000000 INFO @ Fri, 10 Dec 2021 17:12:45: 10000000 INFO @ Fri, 10 Dec 2021 17:12:46: 2000000 INFO @ Fri, 10 Dec 2021 17:12:47: 7000000 INFO @ Fri, 10 Dec 2021 17:12:52: 11000000 INFO @ Fri, 10 Dec 2021 17:12:54: 3000000 INFO @ Fri, 10 Dec 2021 17:12:54: 8000000 INFO @ Fri, 10 Dec 2021 17:13:00: 12000000 INFO @ Fri, 10 Dec 2021 17:13:01: 9000000 INFO @ Fri, 10 Dec 2021 17:13:01: 4000000 INFO @ Fri, 10 Dec 2021 17:13:07: 13000000 INFO @ Fri, 10 Dec 2021 17:13:08: 10000000 INFO @ Fri, 10 Dec 2021 17:13:09: 5000000 INFO @ Fri, 10 Dec 2021 17:13:14: 11000000 INFO @ Fri, 10 Dec 2021 17:13:15: 14000000 INFO @ Fri, 10 Dec 2021 17:13:17: 6000000 INFO @ Fri, 10 Dec 2021 17:13:21: 12000000 INFO @ Fri, 10 Dec 2021 17:13:22: 15000000 INFO @ Fri, 10 Dec 2021 17:13:25: 7000000 INFO @ Fri, 10 Dec 2021 17:13:28: 13000000 INFO @ Fri, 10 Dec 2021 17:13:30: 16000000 INFO @ Fri, 10 Dec 2021 17:13:32: 8000000 INFO @ Fri, 10 Dec 2021 17:13:35: 14000000 INFO @ Fri, 10 Dec 2021 17:13:37: 17000000 INFO @ Fri, 10 Dec 2021 17:13:40: 9000000 INFO @ Fri, 10 Dec 2021 17:13:42: 15000000 INFO @ Fri, 10 Dec 2021 17:13:45: 18000000 INFO @ Fri, 10 Dec 2021 17:13:48: 16000000 INFO @ Fri, 10 Dec 2021 17:13:48: 10000000 INFO @ Fri, 10 Dec 2021 17:13:52: 19000000 INFO @ Fri, 10 Dec 2021 17:13:55: 17000000 INFO @ Fri, 10 Dec 2021 17:13:56: 11000000 INFO @ Fri, 10 Dec 2021 17:13:59: 20000000 INFO @ Fri, 10 Dec 2021 17:14:02: 18000000 INFO @ Fri, 10 Dec 2021 17:14:04: 12000000 INFO @ Fri, 10 Dec 2021 17:14:07: 21000000 INFO @ Fri, 10 Dec 2021 17:14:08: 19000000 INFO @ Fri, 10 Dec 2021 17:14:12: 13000000 INFO @ Fri, 10 Dec 2021 17:14:14: 22000000 INFO @ Fri, 10 Dec 2021 17:14:15: 20000000 INFO @ Fri, 10 Dec 2021 17:14:19: 14000000 INFO @ Fri, 10 Dec 2021 17:14:22: 21000000 INFO @ Fri, 10 Dec 2021 17:14:22: 23000000 INFO @ Fri, 10 Dec 2021 17:14:27: 15000000 INFO @ Fri, 10 Dec 2021 17:14:29: 22000000 INFO @ Fri, 10 Dec 2021 17:14:29: 24000000 INFO @ Fri, 10 Dec 2021 17:14:34: 16000000 INFO @ Fri, 10 Dec 2021 17:14:36: 23000000 INFO @ Fri, 10 Dec 2021 17:14:37: 25000000 INFO @ Fri, 10 Dec 2021 17:14:42: 17000000 INFO @ Fri, 10 Dec 2021 17:14:42: 24000000 INFO @ Fri, 10 Dec 2021 17:14:45: 26000000 INFO @ Fri, 10 Dec 2021 17:14:49: 25000000 INFO @ Fri, 10 Dec 2021 17:14:49: 18000000 INFO @ Fri, 10 Dec 2021 17:14:52: 27000000 INFO @ Fri, 10 Dec 2021 17:14:56: 26000000 INFO @ Fri, 10 Dec 2021 17:14:57: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:15:00: 28000000 INFO @ Fri, 10 Dec 2021 17:15:03: 27000000 INFO @ Fri, 10 Dec 2021 17:15:05: 20000000 INFO @ Fri, 10 Dec 2021 17:15:07: 29000000 INFO @ Fri, 10 Dec 2021 17:15:10: 28000000 INFO @ Fri, 10 Dec 2021 17:15:12: 21000000 INFO @ Fri, 10 Dec 2021 17:15:15: 30000000 INFO @ Fri, 10 Dec 2021 17:15:17: 29000000 INFO @ Fri, 10 Dec 2021 17:15:20: 22000000 INFO @ Fri, 10 Dec 2021 17:15:22: 31000000 INFO @ Fri, 10 Dec 2021 17:15:24: 30000000 INFO @ Fri, 10 Dec 2021 17:15:27: 23000000 INFO @ Fri, 10 Dec 2021 17:15:30: 32000000 INFO @ Fri, 10 Dec 2021 17:15:31: 31000000 INFO @ Fri, 10 Dec 2021 17:15:35: 24000000 INFO @ Fri, 10 Dec 2021 17:15:37: 33000000 INFO @ Fri, 10 Dec 2021 17:15:37: 32000000 INFO @ Fri, 10 Dec 2021 17:15:43: 25000000 INFO @ Fri, 10 Dec 2021 17:15:44: 33000000 INFO @ Fri, 10 Dec 2021 17:15:44: 34000000 INFO @ Fri, 10 Dec 2021 17:15:51: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:15:51: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:15:51: #1 total tags in treatment: 14672445 INFO @ Fri, 10 Dec 2021 17:15:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:15:51: #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 17:15:51: 34000000 INFO @ Fri, 10 Dec 2021 17:15:51: #1 tags after filtering in treatment: 13250757 INFO @ Fri, 10 Dec 2021 17:15:51: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:15:51: #1 finished! INFO @ Fri, 10 Dec 2021 17:15:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:15:52: 26000000 INFO @ Fri, 10 Dec 2021 17:15:52: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 17:15:52: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 17:15:52: start model_add_line... INFO @ Fri, 10 Dec 2021 17:15:52: start X-correlation... INFO @ Fri, 10 Dec 2021 17:15:52: end of X-cor INFO @ Fri, 10 Dec 2021 17:15:52: #2 finished! INFO @ Fri, 10 Dec 2021 17:15:52: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 17:15:52: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 17:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.05_model.r WARNING @ Fri, 10 Dec 2021 17:15:52: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:15:52: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 17:15:52: #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 17:15:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:15:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:15:57: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:15:57: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:15:57: #1 total tags in treatment: 14672445 INFO @ Fri, 10 Dec 2021 17:15:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:15:57: #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 17:15:57: #1 tags after filtering in treatment: 13250757 INFO @ Fri, 10 Dec 2021 17:15:57: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:15:57: #1 finished! INFO @ Fri, 10 Dec 2021 17:15:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:15:58: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 17:15:58: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 17:15:58: start model_add_line... INFO @ Fri, 10 Dec 2021 17:15:58: start X-correlation... INFO @ Fri, 10 Dec 2021 17:15:58: end of X-cor INFO @ Fri, 10 Dec 2021 17:15:58: #2 finished! INFO @ Fri, 10 Dec 2021 17:15:58: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 17:15:58: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 17:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.10_model.r WARNING @ Fri, 10 Dec 2021 17:15:58: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:15:58: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 17:15:58: #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 17:15:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:16:00: 27000000 INFO @ Fri, 10 Dec 2021 17:16:07: 28000000 INFO @ Fri, 10 Dec 2021 17:16:14: 29000000 INFO @ Fri, 10 Dec 2021 17:16:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:16:22: 30000000 INFO @ Fri, 10 Dec 2021 17:16:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:16:29: 31000000 INFO @ Fri, 10 Dec 2021 17:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.05_summits.bed INFO @ Fri, 10 Dec 2021 17:16:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11770 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:16:36: 32000000 INFO @ Fri, 10 Dec 2021 17:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.10_summits.bed INFO @ Fri, 10 Dec 2021 17:16:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6313 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:16:43: 33000000 INFO @ Fri, 10 Dec 2021 17:16:50: 34000000 INFO @ Fri, 10 Dec 2021 17:16:56: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:16:56: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:16:56: #1 total tags in treatment: 14672445 INFO @ Fri, 10 Dec 2021 17:16:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:16:56: #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 17:16:56: #1 tags after filtering in treatment: 13250757 INFO @ Fri, 10 Dec 2021 17:16:56: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 17:16:56: #1 finished! INFO @ Fri, 10 Dec 2021 17:16:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:16:57: #2 number of paired peaks: 658 WARNING @ Fri, 10 Dec 2021 17:16:57: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 10 Dec 2021 17:16:57: start model_add_line... INFO @ Fri, 10 Dec 2021 17:16:57: start X-correlation... INFO @ Fri, 10 Dec 2021 17:16:57: end of X-cor INFO @ Fri, 10 Dec 2021 17:16:57: #2 finished! INFO @ Fri, 10 Dec 2021 17:16:57: #2 predicted fragment length is 154 bps INFO @ Fri, 10 Dec 2021 17:16:57: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 10 Dec 2021 17:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.20_model.r WARNING @ Fri, 10 Dec 2021 17:16:57: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:16:57: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 10 Dec 2021 17:16:57: #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 17:16:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:17:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978934/ERX3978934.20_summits.bed INFO @ Fri, 10 Dec 2021 17:17:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2568 records, 4 fields): 4 millis CompletedMACS2peakCalling