Job ID = 12265374 SRX = SRX6817532 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27982486 spots for SRR10084523/SRR10084523.sra Written 27982486 spots for SRR10084523/SRR10084523.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265902 ("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: 01:29:03 27982486 reads; of these: 27982486 (100.00%) were paired; of these: 12616761 (45.09%) aligned concordantly 0 times 12629787 (45.13%) aligned concordantly exactly 1 time 2735938 (9.78%) aligned concordantly >1 times ---- 12616761 pairs aligned concordantly 0 times; of these: 3529344 (27.97%) aligned discordantly 1 time ---- 9087417 pairs aligned 0 times concordantly or discordantly; of these: 18174834 mates make up the pairs; of these: 15470358 (85.12%) aligned 0 times 998835 (5.50%) aligned exactly 1 time 1705641 (9.38%) aligned >1 times 72.36% overall alignment rate Time searching: 01:29:03 Overall time: 01:29:03 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 32 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] 3339977 / 18814843 = 0.1775 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 08:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.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 08:48:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:48:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:48:56: 1000000 INFO @ Sat, 03 Apr 2021 08:49:06: 2000000 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 08:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.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 08:49:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:49:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:49:16: 3000000 INFO @ Sat, 03 Apr 2021 08:49:26: 4000000 INFO @ Sat, 03 Apr 2021 08:49:28: 1000000 INFO @ Sat, 03 Apr 2021 08:49:37: 5000000 INFO @ Sat, 03 Apr 2021 08:49:42: 2000000 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 08:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.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 08:49:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:49:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:49:48: 6000000 INFO @ Sat, 03 Apr 2021 08:49:56: 3000000 INFO @ Sat, 03 Apr 2021 08:49:58: 1000000 INFO @ Sat, 03 Apr 2021 08:50:02: 7000000 INFO @ Sat, 03 Apr 2021 08:50:09: 4000000 INFO @ Sat, 03 Apr 2021 08:50:11: 2000000 INFO @ Sat, 03 Apr 2021 08:50:15: 8000000 INFO @ Sat, 03 Apr 2021 08:50:24: 5000000 INFO @ Sat, 03 Apr 2021 08:50:25: 3000000 INFO @ Sat, 03 Apr 2021 08:50:29: 9000000 INFO @ Sat, 03 Apr 2021 08:50:37: 6000000 INFO @ Sat, 03 Apr 2021 08:50:39: 4000000 INFO @ Sat, 03 Apr 2021 08:50:43: 10000000 INFO @ Sat, 03 Apr 2021 08:50:52: 7000000 INFO @ Sat, 03 Apr 2021 08:50:52: 5000000 INFO @ Sat, 03 Apr 2021 08:50:56: 11000000 INFO @ Sat, 03 Apr 2021 08:51:05: 6000000 INFO @ Sat, 03 Apr 2021 08:51:05: 8000000 INFO @ Sat, 03 Apr 2021 08:51:09: 12000000 INFO @ Sat, 03 Apr 2021 08:51:18: 7000000 INFO @ Sat, 03 Apr 2021 08:51:20: 9000000 INFO @ Sat, 03 Apr 2021 08:51:22: 13000000 INFO @ Sat, 03 Apr 2021 08:51:31: 8000000 INFO @ Sat, 03 Apr 2021 08:51:33: 10000000 INFO @ Sat, 03 Apr 2021 08:51:35: 14000000 INFO @ Sat, 03 Apr 2021 08:51:44: 9000000 INFO @ Sat, 03 Apr 2021 08:51:47: 11000000 INFO @ Sat, 03 Apr 2021 08:51:48: 15000000 INFO @ Sat, 03 Apr 2021 08:51:57: 10000000 INFO @ Sat, 03 Apr 2021 08:52:00: 12000000 INFO @ Sat, 03 Apr 2021 08:52:01: 16000000 INFO @ Sat, 03 Apr 2021 08:52:11: 11000000 INFO @ Sat, 03 Apr 2021 08:52:14: 13000000 INFO @ Sat, 03 Apr 2021 08:52:15: 17000000 INFO @ Sat, 03 Apr 2021 08:52:25: 12000000 INFO @ Sat, 03 Apr 2021 08:52:28: 14000000 INFO @ Sat, 03 Apr 2021 08:52:28: 18000000 INFO @ Sat, 03 Apr 2021 08:52:37: 13000000 INFO @ Sat, 03 Apr 2021 08:52:40: 19000000 INFO @ Sat, 03 Apr 2021 08:52:41: 15000000 INFO @ Sat, 03 Apr 2021 08:52:50: 14000000 INFO @ Sat, 03 Apr 2021 08:52:53: 20000000 INFO @ Sat, 03 Apr 2021 08:52:54: 16000000 INFO @ Sat, 03 Apr 2021 08:53:03: 15000000 INFO @ Sat, 03 Apr 2021 08:53:06: 21000000 INFO @ Sat, 03 Apr 2021 08:53:07: 17000000 INFO @ Sat, 03 Apr 2021 08:53:15: 16000000 INFO @ Sat, 03 Apr 2021 08:53:18: 22000000 INFO @ Sat, 03 Apr 2021 08:53:21: 18000000 INFO @ Sat, 03 Apr 2021 08:53:27: 17000000 INFO @ Sat, 03 Apr 2021 08:53:31: 23000000 INFO @ Sat, 03 Apr 2021 08:53:34: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:53:38: 18000000 INFO @ Sat, 03 Apr 2021 08:53:43: 24000000 INFO @ Sat, 03 Apr 2021 08:53:47: 20000000 INFO @ Sat, 03 Apr 2021 08:53:51: 19000000 INFO @ Sat, 03 Apr 2021 08:53:55: 25000000 INFO @ Sat, 03 Apr 2021 08:54:02: 21000000 INFO @ Sat, 03 Apr 2021 08:54:03: 20000000 INFO @ Sat, 03 Apr 2021 08:54:07: 26000000 INFO @ Sat, 03 Apr 2021 08:54:15: 22000000 INFO @ Sat, 03 Apr 2021 08:54:16: 21000000 INFO @ Sat, 03 Apr 2021 08:54:19: 27000000 INFO @ Sat, 03 Apr 2021 08:54:28: 23000000 INFO @ Sat, 03 Apr 2021 08:54:28: 22000000 INFO @ Sat, 03 Apr 2021 08:54:32: 28000000 INFO @ Sat, 03 Apr 2021 08:54:41: 24000000 INFO @ Sat, 03 Apr 2021 08:54:41: 23000000 INFO @ Sat, 03 Apr 2021 08:54:45: 29000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:54:52: 25000000 INFO @ Sat, 03 Apr 2021 08:54:54: 24000000 INFO @ Sat, 03 Apr 2021 08:54:58: 30000000 INFO @ Sat, 03 Apr 2021 08:55:04: 26000000 INFO @ Sat, 03 Apr 2021 08:55:06: 25000000 INFO @ Sat, 03 Apr 2021 08:55:11: 31000000 INFO @ Sat, 03 Apr 2021 08:55:15: 27000000 INFO @ Sat, 03 Apr 2021 08:55:18: 26000000 INFO @ Sat, 03 Apr 2021 08:55:24: 32000000 INFO @ Sat, 03 Apr 2021 08:55:27: 28000000 INFO @ Sat, 03 Apr 2021 08:55:31: 27000000 INFO @ Sat, 03 Apr 2021 08:55:36: 33000000 INFO @ Sat, 03 Apr 2021 08:55:39: 29000000 INFO @ Sat, 03 Apr 2021 08:55:43: 28000000 INFO @ Sat, 03 Apr 2021 08:55:46: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:55:46: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:55:46: #1 total tags in treatment: 12451200 INFO @ Sat, 03 Apr 2021 08:55:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:55:46: #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 08:55:46: #1 tags after filtering in treatment: 10260856 INFO @ Sat, 03 Apr 2021 08:55:46: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:55:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:55:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:55:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:55:47: #2 number of paired peaks: 259 WARNING @ Sat, 03 Apr 2021 08:55:47: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sat, 03 Apr 2021 08:55:47: start model_add_line... INFO @ Sat, 03 Apr 2021 08:55:47: start X-correlation... INFO @ Sat, 03 Apr 2021 08:55:47: end of X-cor INFO @ Sat, 03 Apr 2021 08:55:47: #2 finished! INFO @ Sat, 03 Apr 2021 08:55:47: #2 predicted fragment length is 217 bps INFO @ Sat, 03 Apr 2021 08:55:47: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 03 Apr 2021 08:55:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.05_model.r WARNING @ Sat, 03 Apr 2021 08:55:47: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:55:47: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 03 Apr 2021 08:55:47: #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 08:55:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:55:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:55:48: 30000000 INFO @ Sat, 03 Apr 2021 08:55:55: 29000000 INFO @ Sat, 03 Apr 2021 08:55:58: 31000000 INFO @ Sat, 03 Apr 2021 08:56:06: 30000000 INFO @ Sat, 03 Apr 2021 08:56:08: 32000000 INFO @ Sat, 03 Apr 2021 08:56:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:56:17: 31000000 INFO @ Sat, 03 Apr 2021 08:56:18: 33000000 INFO @ Sat, 03 Apr 2021 08:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.05_summits.bed INFO @ Sat, 03 Apr 2021 08:56:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6096 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:56:25: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:56:25: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:56:25: #1 total tags in treatment: 12451200 INFO @ Sat, 03 Apr 2021 08:56:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:56:25: #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 08:56:25: #1 tags after filtering in treatment: 10260856 INFO @ Sat, 03 Apr 2021 08:56:25: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:56:25: #1 finished! INFO @ Sat, 03 Apr 2021 08:56:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:56:26: #2 number of paired peaks: 259 WARNING @ Sat, 03 Apr 2021 08:56:26: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sat, 03 Apr 2021 08:56:26: start model_add_line... INFO @ Sat, 03 Apr 2021 08:56:26: start X-correlation... INFO @ Sat, 03 Apr 2021 08:56:26: end of X-cor INFO @ Sat, 03 Apr 2021 08:56:26: #2 finished! INFO @ Sat, 03 Apr 2021 08:56:26: #2 predicted fragment length is 217 bps INFO @ Sat, 03 Apr 2021 08:56:26: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 03 Apr 2021 08:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.10_model.r WARNING @ Sat, 03 Apr 2021 08:56:26: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:56:26: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 03 Apr 2021 08:56:26: #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 08:56:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:56:28: 32000000 INFO @ Sat, 03 Apr 2021 08:56:38: 33000000 INFO @ Sat, 03 Apr 2021 08:56:46: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:56:46: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:56:46: #1 total tags in treatment: 12451200 INFO @ Sat, 03 Apr 2021 08:56:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:56:46: #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 08:56:46: #1 tags after filtering in treatment: 10260856 INFO @ Sat, 03 Apr 2021 08:56:46: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:56:46: #1 finished! INFO @ Sat, 03 Apr 2021 08:56:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:56:47: #2 number of paired peaks: 259 WARNING @ Sat, 03 Apr 2021 08:56:47: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sat, 03 Apr 2021 08:56:47: start model_add_line... INFO @ Sat, 03 Apr 2021 08:56:47: start X-correlation... INFO @ Sat, 03 Apr 2021 08:56:47: end of X-cor INFO @ Sat, 03 Apr 2021 08:56:47: #2 finished! INFO @ Sat, 03 Apr 2021 08:56:47: #2 predicted fragment length is 217 bps INFO @ Sat, 03 Apr 2021 08:56:47: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 03 Apr 2021 08:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.20_model.r WARNING @ Sat, 03 Apr 2021 08:56:47: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:56:47: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 03 Apr 2021 08:56:47: #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 08:56:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:56:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.10_summits.bed INFO @ Sat, 03 Apr 2021 08:56:59: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2419 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:57:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817532/SRX6817532.20_summits.bed INFO @ Sat, 03 Apr 2021 08:57:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 2 millis CompletedMACS2peakCalling