Job ID = 14170129 SRX = SRX8556260 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34540461 spots for SRR12024634/SRR12024634.sra Written 34540461 spots for SRR12024634/SRR12024634.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170812 ("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: 00:58:35 34540461 reads; of these: 34540461 (100.00%) were paired; of these: 28457586 (82.39%) aligned concordantly 0 times 4931514 (14.28%) aligned concordantly exactly 1 time 1151361 (3.33%) aligned concordantly >1 times ---- 28457586 pairs aligned concordantly 0 times; of these: 1632482 (5.74%) aligned discordantly 1 time ---- 26825104 pairs aligned 0 times concordantly or discordantly; of these: 53650208 mates make up the pairs; of these: 52451065 (97.76%) aligned 0 times 416787 (0.78%) aligned exactly 1 time 782356 (1.46%) aligned >1 times 24.07% overall alignment rate Time searching: 00:58:35 Overall time: 00:58:35 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 16 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] 527263 / 7669163 = 0.0688 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 @ Sat, 11 Dec 2021 06:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.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, 11 Dec 2021 06:58:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:58:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:58:56: 1000000 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 @ Sat, 11 Dec 2021 06:59:11: 2000000 INFO @ Sat, 11 Dec 2021 06:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.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, 11 Dec 2021 06:59:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:59:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:59:26: 3000000 INFO @ Sat, 11 Dec 2021 06:59:27: 1000000 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 @ Sat, 11 Dec 2021 06:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.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, 11 Dec 2021 06:59:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:59:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:59:42: 4000000 INFO @ Sat, 11 Dec 2021 06:59:43: 2000000 INFO @ Sat, 11 Dec 2021 06:59:57: 5000000 INFO @ Sat, 11 Dec 2021 06:59:59: 1000000 INFO @ Sat, 11 Dec 2021 06:59:59: 3000000 INFO @ Sat, 11 Dec 2021 07:00:13: 6000000 INFO @ Sat, 11 Dec 2021 07:00:15: 4000000 INFO @ Sat, 11 Dec 2021 07:00:16: 2000000 INFO @ Sat, 11 Dec 2021 07:00:29: 7000000 INFO @ Sat, 11 Dec 2021 07:00:31: 5000000 INFO @ Sat, 11 Dec 2021 07:00:34: 3000000 INFO @ Sat, 11 Dec 2021 07:00:44: 8000000 INFO @ Sat, 11 Dec 2021 07:00:47: 6000000 INFO @ Sat, 11 Dec 2021 07:00:50: 4000000 INFO @ Sat, 11 Dec 2021 07:00:59: 9000000 INFO @ Sat, 11 Dec 2021 07:01:03: 7000000 INFO @ Sat, 11 Dec 2021 07:01:08: 5000000 INFO @ Sat, 11 Dec 2021 07:01:15: 10000000 INFO @ Sat, 11 Dec 2021 07:01:18: 8000000 INFO @ Sat, 11 Dec 2021 07:01:25: 6000000 INFO @ Sat, 11 Dec 2021 07:01:30: 11000000 INFO @ Sat, 11 Dec 2021 07:01:34: 9000000 INFO @ Sat, 11 Dec 2021 07:01:42: 7000000 INFO @ Sat, 11 Dec 2021 07:01:46: 12000000 INFO @ Sat, 11 Dec 2021 07:01:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:01:59: 8000000 INFO @ Sat, 11 Dec 2021 07:02:02: 13000000 INFO @ Sat, 11 Dec 2021 07:02:06: 11000000 INFO @ Sat, 11 Dec 2021 07:02:16: 9000000 INFO @ Sat, 11 Dec 2021 07:02:17: 14000000 INFO @ Sat, 11 Dec 2021 07:02:22: 12000000 INFO @ Sat, 11 Dec 2021 07:02:33: 10000000 INFO @ Sat, 11 Dec 2021 07:02:33: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:02:37: 13000000 INFO @ Sat, 11 Dec 2021 07:02:42: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:02:42: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:02:42: #1 total tags in treatment: 5643915 INFO @ Sat, 11 Dec 2021 07:02:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:02:42: #1 tags after filtering in treatment: 5108087 INFO @ Sat, 11 Dec 2021 07:02:42: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 07:02:42: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:43: #2 number of paired peaks: 593 WARNING @ Sat, 11 Dec 2021 07:02:43: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:43: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:43: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:43: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:43: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:43: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 07:02:43: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 11 Dec 2021 07:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.05_model.r WARNING @ Sat, 11 Dec 2021 07:02:43: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:02:43: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 11 Dec 2021 07:02:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:02:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:02:50: 11000000 INFO @ Sat, 11 Dec 2021 07:02:53: 14000000 INFO @ Sat, 11 Dec 2021 07:02:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:03:07: 12000000 INFO @ Sat, 11 Dec 2021 07:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.05_summits.bed INFO @ Sat, 11 Dec 2021 07:03:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2957 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:03:09: 15000000 INFO @ Sat, 11 Dec 2021 07:03:18: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:03:18: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:03:18: #1 total tags in treatment: 5643915 INFO @ Sat, 11 Dec 2021 07:03:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:03:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:03:18: #1 tags after filtering in treatment: 5108087 INFO @ Sat, 11 Dec 2021 07:03:18: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 07:03:18: #1 finished! INFO @ Sat, 11 Dec 2021 07:03:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:03:19: #2 number of paired peaks: 593 WARNING @ Sat, 11 Dec 2021 07:03:19: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 11 Dec 2021 07:03:19: start model_add_line... INFO @ Sat, 11 Dec 2021 07:03:19: start X-correlation... INFO @ Sat, 11 Dec 2021 07:03:19: end of X-cor INFO @ Sat, 11 Dec 2021 07:03:19: #2 finished! INFO @ Sat, 11 Dec 2021 07:03:19: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 07:03:19: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 11 Dec 2021 07:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.10_model.r WARNING @ Sat, 11 Dec 2021 07:03:19: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:03:19: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 11 Dec 2021 07:03:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:03:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:03:24: 13000000 INFO @ Sat, 11 Dec 2021 07:03:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:03:40: 14000000 INFO @ Sat, 11 Dec 2021 07:03:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:03:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:03:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.10_summits.bed INFO @ Sat, 11 Dec 2021 07:03:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1055 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:03:56: 15000000 INFO @ Sat, 11 Dec 2021 07:04:05: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:04:05: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:04:05: #1 total tags in treatment: 5643915 INFO @ Sat, 11 Dec 2021 07:04:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:04:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:04:05: #1 tags after filtering in treatment: 5108087 INFO @ Sat, 11 Dec 2021 07:04:05: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 07:04:05: #1 finished! INFO @ Sat, 11 Dec 2021 07:04:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:04:05: #2 number of paired peaks: 593 WARNING @ Sat, 11 Dec 2021 07:04:05: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 11 Dec 2021 07:04:05: start model_add_line... INFO @ Sat, 11 Dec 2021 07:04:06: start X-correlation... INFO @ Sat, 11 Dec 2021 07:04:06: end of X-cor INFO @ Sat, 11 Dec 2021 07:04:06: #2 finished! INFO @ Sat, 11 Dec 2021 07:04:06: #2 predicted fragment length is 219 bps INFO @ Sat, 11 Dec 2021 07:04:06: #2 alternative fragment length(s) may be 219 bps INFO @ Sat, 11 Dec 2021 07:04:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.20_model.r WARNING @ Sat, 11 Dec 2021 07:04:06: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:04:06: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Sat, 11 Dec 2021 07:04:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:04:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:04:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:04:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556260/SRX8556260.20_summits.bed INFO @ Sat, 11 Dec 2021 07:04:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 3 millis CompletedMACS2peakCalling