Job ID = 6626508 SRX = SRX5736485 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8260507 spots for SRR8956896/SRR8956896.sra Written 8260507 spots for SRR8956896/SRR8956896.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626663 ("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: 00:13:52 8260507 reads; of these: 8260507 (100.00%) were paired; of these: 2769233 (33.52%) aligned concordantly 0 times 4346188 (52.61%) aligned concordantly exactly 1 time 1145086 (13.86%) aligned concordantly >1 times ---- 2769233 pairs aligned concordantly 0 times; of these: 682837 (24.66%) aligned discordantly 1 time ---- 2086396 pairs aligned 0 times concordantly or discordantly; of these: 4172792 mates make up the pairs; of these: 3398920 (81.45%) aligned 0 times 406378 (9.74%) aligned exactly 1 time 367494 (8.81%) aligned >1 times 79.43% overall alignment rate Time searching: 00:13:52 Overall time: 00:13:52 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] 660942 / 6106735 = 0.1082 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.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, 14 Jul 2020 07:29:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:02: 1000000 INFO @ Tue, 14 Jul 2020 07:30:09: 2000000 INFO @ Tue, 14 Jul 2020 07:30:16: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:30:24: 4000000 INFO @ Tue, 14 Jul 2020 07:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.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, 14 Jul 2020 07:30:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:30:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:31: 5000000 INFO @ Tue, 14 Jul 2020 07:30:32: 1000000 INFO @ Tue, 14 Jul 2020 07:30:40: 6000000 INFO @ Tue, 14 Jul 2020 07:30:41: 2000000 INFO @ Tue, 14 Jul 2020 07:30:49: 7000000 INFO @ Tue, 14 Jul 2020 07:30:49: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 07:30:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.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, 14 Jul 2020 07:30:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:30:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:58: 8000000 INFO @ Tue, 14 Jul 2020 07:30:59: 4000000 INFO @ Tue, 14 Jul 2020 07:31:01: 1000000 INFO @ Tue, 14 Jul 2020 07:31:08: 9000000 INFO @ Tue, 14 Jul 2020 07:31:08: 5000000 INFO @ Tue, 14 Jul 2020 07:31:09: 2000000 INFO @ Tue, 14 Jul 2020 07:31:16: 3000000 INFO @ Tue, 14 Jul 2020 07:31:17: 10000000 INFO @ Tue, 14 Jul 2020 07:31:18: 6000000 INFO @ Tue, 14 Jul 2020 07:31:23: 4000000 INFO @ Tue, 14 Jul 2020 07:31:27: 11000000 INFO @ Tue, 14 Jul 2020 07:31:28: 7000000 INFO @ Tue, 14 Jul 2020 07:31:30: 5000000 INFO @ Tue, 14 Jul 2020 07:31:34: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:31:34: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:31:34: #1 total tags in treatment: 4907955 INFO @ Tue, 14 Jul 2020 07:31:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:31:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:31:35: #1 tags after filtering in treatment: 4459881 INFO @ Tue, 14 Jul 2020 07:31:35: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 07:31:35: #1 finished! INFO @ Tue, 14 Jul 2020 07:31:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:31:35: #2 number of paired peaks: 434 WARNING @ Tue, 14 Jul 2020 07:31:35: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 14 Jul 2020 07:31:35: start model_add_line... INFO @ Tue, 14 Jul 2020 07:31:35: start X-correlation... INFO @ Tue, 14 Jul 2020 07:31:35: end of X-cor INFO @ Tue, 14 Jul 2020 07:31:35: #2 finished! INFO @ Tue, 14 Jul 2020 07:31:35: #2 predicted fragment length is 144 bps INFO @ Tue, 14 Jul 2020 07:31:35: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 14 Jul 2020 07:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.05_model.r WARNING @ Tue, 14 Jul 2020 07:31:35: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:31:35: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 14 Jul 2020 07:31:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:31:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:31:37: 8000000 INFO @ Tue, 14 Jul 2020 07:31:37: 6000000 INFO @ Tue, 14 Jul 2020 07:31:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:31:44: 7000000 INFO @ Tue, 14 Jul 2020 07:31:46: 9000000 INFO @ Tue, 14 Jul 2020 07:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.05_summits.bed INFO @ Tue, 14 Jul 2020 07:31:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1782 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:31:51: 8000000 INFO @ Tue, 14 Jul 2020 07:31:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:31:59: 9000000 INFO @ Tue, 14 Jul 2020 07:32:04: 11000000 INFO @ Tue, 14 Jul 2020 07:32:06: 10000000 INFO @ Tue, 14 Jul 2020 07:32:11: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:32:11: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:32:11: #1 total tags in treatment: 4907955 INFO @ Tue, 14 Jul 2020 07:32:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:32:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:32:11: #1 tags after filtering in treatment: 4459881 INFO @ Tue, 14 Jul 2020 07:32:11: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 07:32:11: #1 finished! INFO @ Tue, 14 Jul 2020 07:32:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:32:11: #2 number of paired peaks: 434 WARNING @ Tue, 14 Jul 2020 07:32:11: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 14 Jul 2020 07:32:11: start model_add_line... INFO @ Tue, 14 Jul 2020 07:32:11: start X-correlation... INFO @ Tue, 14 Jul 2020 07:32:12: end of X-cor INFO @ Tue, 14 Jul 2020 07:32:12: #2 finished! INFO @ Tue, 14 Jul 2020 07:32:12: #2 predicted fragment length is 144 bps INFO @ Tue, 14 Jul 2020 07:32:12: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 14 Jul 2020 07:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.10_model.r WARNING @ Tue, 14 Jul 2020 07:32:12: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:32:12: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 14 Jul 2020 07:32:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:32:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:32:13: 11000000 INFO @ Tue, 14 Jul 2020 07:32:18: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:32:18: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:32:18: #1 total tags in treatment: 4907955 INFO @ Tue, 14 Jul 2020 07:32:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:32:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:32:18: #1 tags after filtering in treatment: 4459881 INFO @ Tue, 14 Jul 2020 07:32:18: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 07:32:18: #1 finished! INFO @ Tue, 14 Jul 2020 07:32:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:32:18: #2 number of paired peaks: 434 WARNING @ Tue, 14 Jul 2020 07:32:18: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 14 Jul 2020 07:32:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:32:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:32:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:32:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:32:18: #2 predicted fragment length is 144 bps INFO @ Tue, 14 Jul 2020 07:32:18: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 14 Jul 2020 07:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.20_model.r WARNING @ Tue, 14 Jul 2020 07:32:18: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:32:18: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 14 Jul 2020 07:32:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:32:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:32:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:32:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:32:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:32:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:32:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.10_summits.bed INFO @ Tue, 14 Jul 2020 07:32:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (742 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:32:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736485/SRX5736485.20_summits.bed INFO @ Tue, 14 Jul 2020 07:32:32: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (415 records, 4 fields): 19 millis CompletedMACS2peakCalling