Job ID = 16439581 SRX = SRX9518334 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8729860 spots for SRR13070817/SRR13070817.sra Written 8729860 spots for SRR13070817/SRR13070817.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439683 ("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: 00:15:50 8729860 reads; of these: 8729860 (100.00%) were paired; of these: 643059 (7.37%) aligned concordantly 0 times 3095618 (35.46%) aligned concordantly exactly 1 time 4991183 (57.17%) aligned concordantly >1 times ---- 643059 pairs aligned concordantly 0 times; of these: 126347 (19.65%) aligned discordantly 1 time ---- 516712 pairs aligned 0 times concordantly or discordantly; of these: 1033424 mates make up the pairs; of these: 408363 (39.52%) aligned 0 times 95157 (9.21%) aligned exactly 1 time 529904 (51.28%) aligned >1 times 97.66% overall alignment rate Time searching: 00:15:50 Overall time: 00:15:50 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 8 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] 1742062 / 8182487 = 0.2129 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:55:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.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 @ Tue, 02 Aug 2022 15:55:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:55:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:55:31: 1000000 INFO @ Tue, 02 Aug 2022 15:55:37: 2000000 INFO @ Tue, 02 Aug 2022 15:55:43: 3000000 INFO @ Tue, 02 Aug 2022 15:55:49: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:55:54: 5000000 INFO @ Tue, 02 Aug 2022 15:55:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.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 @ Tue, 02 Aug 2022 15:55:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:55:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:56:01: 6000000 INFO @ Tue, 02 Aug 2022 15:56:01: 1000000 INFO @ Tue, 02 Aug 2022 15:56:07: 7000000 INFO @ Tue, 02 Aug 2022 15:56:08: 2000000 INFO @ Tue, 02 Aug 2022 15:56:13: 8000000 INFO @ Tue, 02 Aug 2022 15:56:14: 3000000 INFO @ Tue, 02 Aug 2022 15:56:19: 9000000 INFO @ Tue, 02 Aug 2022 15:56:21: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:56:25: 10000000 INFO @ Tue, 02 Aug 2022 15:56:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.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 @ Tue, 02 Aug 2022 15:56:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:56:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:56:27: 5000000 INFO @ Tue, 02 Aug 2022 15:56:31: 11000000 INFO @ Tue, 02 Aug 2022 15:56:32: 1000000 INFO @ Tue, 02 Aug 2022 15:56:34: 6000000 INFO @ Tue, 02 Aug 2022 15:56:38: 12000000 INFO @ Tue, 02 Aug 2022 15:56:39: 2000000 INFO @ Tue, 02 Aug 2022 15:56:40: 7000000 INFO @ Tue, 02 Aug 2022 15:56:45: 13000000 INFO @ Tue, 02 Aug 2022 15:56:46: 8000000 INFO @ Tue, 02 Aug 2022 15:56:47: 3000000 INFO @ Tue, 02 Aug 2022 15:56:49: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:56:49: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:56:49: #1 total tags in treatment: 6348684 INFO @ Tue, 02 Aug 2022 15:56:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:56:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:56:49: #1 tags after filtering in treatment: 4074293 INFO @ Tue, 02 Aug 2022 15:56:49: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:56:49: #1 finished! INFO @ Tue, 02 Aug 2022 15:56:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:56:49: #2 number of paired peaks: 205 WARNING @ Tue, 02 Aug 2022 15:56:49: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 02 Aug 2022 15:56:49: start model_add_line... INFO @ Tue, 02 Aug 2022 15:56:49: start X-correlation... INFO @ Tue, 02 Aug 2022 15:56:49: end of X-cor INFO @ Tue, 02 Aug 2022 15:56:49: #2 finished! INFO @ Tue, 02 Aug 2022 15:56:49: #2 predicted fragment length is 151 bps INFO @ Tue, 02 Aug 2022 15:56:49: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 02 Aug 2022 15:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.05_model.r WARNING @ Tue, 02 Aug 2022 15:56:49: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:56:49: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Tue, 02 Aug 2022 15:56:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:56:49: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:56:52: 9000000 INFO @ Tue, 02 Aug 2022 15:56:54: 4000000 INFO @ Tue, 02 Aug 2022 15:56:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:56:59: 10000000 INFO @ Tue, 02 Aug 2022 15:57:01: 5000000 INFO @ Tue, 02 Aug 2022 15:57:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.05_summits.bed INFO @ Tue, 02 Aug 2022 15:57:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (886 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:57:05: 11000000 INFO @ Tue, 02 Aug 2022 15:57:08: 6000000 INFO @ Tue, 02 Aug 2022 15:57:11: 12000000 INFO @ Tue, 02 Aug 2022 15:57:15: 7000000 INFO @ Tue, 02 Aug 2022 15:57:18: 13000000 INFO @ Tue, 02 Aug 2022 15:57:22: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:57:22: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:57:22: #1 total tags in treatment: 6348684 INFO @ Tue, 02 Aug 2022 15:57:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:57:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:57:22: #1 tags after filtering in treatment: 4074293 INFO @ Tue, 02 Aug 2022 15:57:22: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:57:22: #1 finished! INFO @ Tue, 02 Aug 2022 15:57:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:57:22: #2 number of paired peaks: 205 WARNING @ Tue, 02 Aug 2022 15:57:22: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 02 Aug 2022 15:57:22: start model_add_line... INFO @ Tue, 02 Aug 2022 15:57:22: start X-correlation... INFO @ Tue, 02 Aug 2022 15:57:22: end of X-cor INFO @ Tue, 02 Aug 2022 15:57:22: #2 finished! INFO @ Tue, 02 Aug 2022 15:57:22: #2 predicted fragment length is 151 bps INFO @ Tue, 02 Aug 2022 15:57:22: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 02 Aug 2022 15:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.10_model.r WARNING @ Tue, 02 Aug 2022 15:57:22: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:57:22: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Tue, 02 Aug 2022 15:57:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:57:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:57:22: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:57:29: 9000000 INFO @ Tue, 02 Aug 2022 15:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:57:35: 10000000 INFO @ Tue, 02 Aug 2022 15:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.10_summits.bed INFO @ Tue, 02 Aug 2022 15:57:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:57:42: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:57:49: 12000000 INFO @ Tue, 02 Aug 2022 15:57:55: 13000000 INFO @ Tue, 02 Aug 2022 15:57:59: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:57:59: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:57:59: #1 total tags in treatment: 6348684 INFO @ Tue, 02 Aug 2022 15:57:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:57:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:57:59: #1 tags after filtering in treatment: 4074293 INFO @ Tue, 02 Aug 2022 15:57:59: #1 Redundant rate of treatment: 0.36 INFO @ Tue, 02 Aug 2022 15:57:59: #1 finished! INFO @ Tue, 02 Aug 2022 15:57:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:57:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:58:00: #2 number of paired peaks: 205 WARNING @ Tue, 02 Aug 2022 15:58:00: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 02 Aug 2022 15:58:00: start model_add_line... INFO @ Tue, 02 Aug 2022 15:58:00: start X-correlation... INFO @ Tue, 02 Aug 2022 15:58:00: end of X-cor INFO @ Tue, 02 Aug 2022 15:58:00: #2 finished! INFO @ Tue, 02 Aug 2022 15:58:00: #2 predicted fragment length is 151 bps INFO @ Tue, 02 Aug 2022 15:58:00: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 02 Aug 2022 15:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.20_model.r WARNING @ Tue, 02 Aug 2022 15:58:00: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:58:00: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Tue, 02 Aug 2022 15:58:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:58:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:58:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518334/SRX9518334.20_summits.bed INFO @ Tue, 02 Aug 2022 15:58:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 29 millis CompletedMACS2peakCalling