Job ID = 14168330 SRX = ERX3978850 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14553997 spots for ERR3975919/ERR3975919.sra Written 14553997 spots for ERR3975919/ERR3975919.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169514 ("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: 00:38:07 14553997 reads; of these: 14553997 (100.00%) were paired; of these: 1501808 (10.32%) aligned concordantly 0 times 10031959 (68.93%) aligned concordantly exactly 1 time 3020230 (20.75%) aligned concordantly >1 times ---- 1501808 pairs aligned concordantly 0 times; of these: 265420 (17.67%) aligned discordantly 1 time ---- 1236388 pairs aligned 0 times concordantly or discordantly; of these: 2472776 mates make up the pairs; of these: 1190187 (48.13%) aligned 0 times 632780 (25.59%) aligned exactly 1 time 649809 (26.28%) aligned >1 times 95.91% overall alignment rate Time searching: 00:38:08 Overall time: 00:38:08 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 12 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] 8416782 / 13278441 = 0.6339 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 18:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.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 18:12:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:12:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:12:26: 1000000 INFO @ Fri, 10 Dec 2021 18:12:33: 2000000 INFO @ Fri, 10 Dec 2021 18:12:40: 3000000 INFO @ Fri, 10 Dec 2021 18:12:46: 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 18:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.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 18:12:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:12:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:12:54: 5000000 INFO @ Fri, 10 Dec 2021 18:12:57: 1000000 INFO @ Fri, 10 Dec 2021 18:13:01: 6000000 INFO @ Fri, 10 Dec 2021 18:13:05: 2000000 INFO @ Fri, 10 Dec 2021 18:13:09: 7000000 INFO @ Fri, 10 Dec 2021 18:13:13: 3000000 INFO @ Fri, 10 Dec 2021 18:13:16: 8000000 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 18:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.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 18:13:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:13:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:13:20: 4000000 INFO @ Fri, 10 Dec 2021 18:13:24: 9000000 INFO @ Fri, 10 Dec 2021 18:13:27: 1000000 INFO @ Fri, 10 Dec 2021 18:13:28: 5000000 INFO @ Fri, 10 Dec 2021 18:13:31: 10000000 INFO @ Fri, 10 Dec 2021 18:13:34: 2000000 INFO @ Fri, 10 Dec 2021 18:13:36: 6000000 INFO @ Fri, 10 Dec 2021 18:13:39: 11000000 INFO @ Fri, 10 Dec 2021 18:13:39: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:13:39: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:13:39: #1 total tags in treatment: 4753020 INFO @ Fri, 10 Dec 2021 18:13:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:13:39: #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 18:13:40: #1 tags after filtering in treatment: 4403706 INFO @ Fri, 10 Dec 2021 18:13:40: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:13:40: #1 finished! INFO @ Fri, 10 Dec 2021 18:13:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:13:40: #2 number of paired peaks: 884 WARNING @ Fri, 10 Dec 2021 18:13:40: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Fri, 10 Dec 2021 18:13:40: start model_add_line... INFO @ Fri, 10 Dec 2021 18:13:40: start X-correlation... INFO @ Fri, 10 Dec 2021 18:13:40: end of X-cor INFO @ Fri, 10 Dec 2021 18:13:40: #2 finished! INFO @ Fri, 10 Dec 2021 18:13:40: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Dec 2021 18:13:40: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Dec 2021 18:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.05_model.r WARNING @ Fri, 10 Dec 2021 18:13:40: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:13:40: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 10 Dec 2021 18:13:40: #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 18:13:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:13:42: 3000000 INFO @ Fri, 10 Dec 2021 18:13:44: 7000000 INFO @ Fri, 10 Dec 2021 18:13:50: 4000000 INFO @ Fri, 10 Dec 2021 18:13:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:13:52: 8000000 INFO @ Fri, 10 Dec 2021 18:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.05_summits.bed INFO @ Fri, 10 Dec 2021 18:13:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3312 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:13:57: 5000000 INFO @ Fri, 10 Dec 2021 18:13:59: 9000000 INFO @ Fri, 10 Dec 2021 18:14:05: 6000000 INFO @ Fri, 10 Dec 2021 18:14:07: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:14:12: 7000000 INFO @ Fri, 10 Dec 2021 18:14:15: 11000000 INFO @ Fri, 10 Dec 2021 18:14:16: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:14:16: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:14:16: #1 total tags in treatment: 4753020 INFO @ Fri, 10 Dec 2021 18:14:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:14:16: #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 18:14:16: #1 tags after filtering in treatment: 4403706 INFO @ Fri, 10 Dec 2021 18:14:16: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:14:16: #1 finished! INFO @ Fri, 10 Dec 2021 18:14:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:14:16: #2 number of paired peaks: 884 WARNING @ Fri, 10 Dec 2021 18:14:16: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Fri, 10 Dec 2021 18:14:16: start model_add_line... INFO @ Fri, 10 Dec 2021 18:14:16: start X-correlation... INFO @ Fri, 10 Dec 2021 18:14:16: end of X-cor INFO @ Fri, 10 Dec 2021 18:14:16: #2 finished! INFO @ Fri, 10 Dec 2021 18:14:16: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Dec 2021 18:14:16: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Dec 2021 18:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.10_model.r WARNING @ Fri, 10 Dec 2021 18:14:16: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:14:16: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 10 Dec 2021 18:14:16: #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 18:14:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:14:20: 8000000 INFO @ Fri, 10 Dec 2021 18:14:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:27: 9000000 INFO @ Fri, 10 Dec 2021 18:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.10_summits.bed INFO @ Fri, 10 Dec 2021 18:14:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1423 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:14:34: 10000000 INFO @ Fri, 10 Dec 2021 18:14:41: 11000000 INFO @ Fri, 10 Dec 2021 18:14:41: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 18:14:41: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 18:14:41: #1 total tags in treatment: 4753020 INFO @ Fri, 10 Dec 2021 18:14:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:14:41: #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 18:14:41: #1 tags after filtering in treatment: 4403706 INFO @ Fri, 10 Dec 2021 18:14:41: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 10 Dec 2021 18:14:41: #1 finished! INFO @ Fri, 10 Dec 2021 18:14:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:14:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:14:42: #2 number of paired peaks: 884 WARNING @ Fri, 10 Dec 2021 18:14:42: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Fri, 10 Dec 2021 18:14:42: start model_add_line... INFO @ Fri, 10 Dec 2021 18:14:42: start X-correlation... INFO @ Fri, 10 Dec 2021 18:14:42: end of X-cor INFO @ Fri, 10 Dec 2021 18:14:42: #2 finished! INFO @ Fri, 10 Dec 2021 18:14:42: #2 predicted fragment length is 146 bps INFO @ Fri, 10 Dec 2021 18:14:42: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 10 Dec 2021 18:14:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.20_model.r WARNING @ Fri, 10 Dec 2021 18:14:42: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:14:42: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Fri, 10 Dec 2021 18:14:42: #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 18:14:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:14:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:14:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:14:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:14:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:14:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978850/ERX3978850.20_summits.bed INFO @ Fri, 10 Dec 2021 18:14:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 2 millis CompletedMACS2peakCalling