Job ID = 14170588 SRX = SRX8497046 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14404703 spots for SRR11952645/SRR11952645.sra Written 14404703 spots for SRR11952645/SRR11952645.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171054 ("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: 00:21:30 14404703 reads; of these: 14404703 (100.00%) were paired; of these: 1086436 (7.54%) aligned concordantly 0 times 3031350 (21.04%) aligned concordantly exactly 1 time 10286917 (71.41%) aligned concordantly >1 times ---- 1086436 pairs aligned concordantly 0 times; of these: 121833 (11.21%) aligned discordantly 1 time ---- 964603 pairs aligned 0 times concordantly or discordantly; of these: 1929206 mates make up the pairs; of these: 831038 (43.08%) aligned 0 times 132661 (6.88%) aligned exactly 1 time 965507 (50.05%) aligned >1 times 97.12% overall alignment rate Time searching: 00:21:30 Overall time: 00:21:30 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] 5772184 / 13398453 = 0.4308 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 07:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.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 07:50:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:50:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:51:05: 1000000 INFO @ Sat, 11 Dec 2021 07:51:13: 2000000 INFO @ Sat, 11 Dec 2021 07:51:20: 3000000 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 07:51:27: 4000000 INFO @ Sat, 11 Dec 2021 07:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.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 07:51:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:51:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:51:34: 5000000 INFO @ Sat, 11 Dec 2021 07:51:35: 1000000 INFO @ Sat, 11 Dec 2021 07:51:41: 6000000 INFO @ Sat, 11 Dec 2021 07:51:43: 2000000 INFO @ Sat, 11 Dec 2021 07:51:48: 7000000 INFO @ Sat, 11 Dec 2021 07:51:50: 3000000 INFO @ Sat, 11 Dec 2021 07:51:55: 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 @ Sat, 11 Dec 2021 07:51:58: 4000000 INFO @ Sat, 11 Dec 2021 07:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.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 07:51:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:51:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:52:02: 9000000 INFO @ Sat, 11 Dec 2021 07:52:05: 5000000 INFO @ Sat, 11 Dec 2021 07:52:06: 1000000 INFO @ Sat, 11 Dec 2021 07:52:09: 10000000 INFO @ Sat, 11 Dec 2021 07:52:12: 6000000 INFO @ Sat, 11 Dec 2021 07:52:13: 2000000 INFO @ Sat, 11 Dec 2021 07:52:17: 11000000 INFO @ Sat, 11 Dec 2021 07:52:19: 7000000 INFO @ Sat, 11 Dec 2021 07:52:21: 3000000 INFO @ Sat, 11 Dec 2021 07:52:24: 12000000 INFO @ Sat, 11 Dec 2021 07:52:26: 8000000 INFO @ Sat, 11 Dec 2021 07:52:28: 4000000 INFO @ Sat, 11 Dec 2021 07:52:31: 13000000 INFO @ Sat, 11 Dec 2021 07:52:33: 9000000 INFO @ Sat, 11 Dec 2021 07:52:35: 5000000 INFO @ Sat, 11 Dec 2021 07:52:38: 14000000 INFO @ Sat, 11 Dec 2021 07:52:40: 10000000 INFO @ Sat, 11 Dec 2021 07:52:43: 6000000 INFO @ Sat, 11 Dec 2021 07:52:45: 15000000 INFO @ Sat, 11 Dec 2021 07:52:48: 11000000 INFO @ Sat, 11 Dec 2021 07:52:50: 7000000 INFO @ Sat, 11 Dec 2021 07:52:53: 16000000 INFO @ Sat, 11 Dec 2021 07:52:55: 12000000 INFO @ Sat, 11 Dec 2021 07:52:56: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:52:56: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:52:56: #1 total tags in treatment: 7553343 INFO @ Sat, 11 Dec 2021 07:52:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:52:56: #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 07:52:56: #1 tags after filtering in treatment: 3844614 INFO @ Sat, 11 Dec 2021 07:52:56: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 11 Dec 2021 07:52:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:52:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:52:56: #2 number of paired peaks: 217 WARNING @ Sat, 11 Dec 2021 07:52:56: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sat, 11 Dec 2021 07:52:56: start model_add_line... INFO @ Sat, 11 Dec 2021 07:52:56: start X-correlation... INFO @ Sat, 11 Dec 2021 07:52:56: end of X-cor INFO @ Sat, 11 Dec 2021 07:52:56: #2 finished! INFO @ Sat, 11 Dec 2021 07:52:56: #2 predicted fragment length is 151 bps INFO @ Sat, 11 Dec 2021 07:52:56: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 11 Dec 2021 07:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.05_model.r WARNING @ Sat, 11 Dec 2021 07:52:56: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:52:56: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sat, 11 Dec 2021 07:52:56: #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 07:52:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:52:57: 8000000 INFO @ Sat, 11 Dec 2021 07:53:02: 13000000 INFO @ Sat, 11 Dec 2021 07:53:04: 9000000 INFO @ Sat, 11 Dec 2021 07:53:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:53:09: 14000000 INFO @ Sat, 11 Dec 2021 07:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.05_summits.bed INFO @ Sat, 11 Dec 2021 07:53:09: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (947 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:53:11: 10000000 INFO @ Sat, 11 Dec 2021 07:53:16: 15000000 INFO @ Sat, 11 Dec 2021 07:53:18: 11000000 INFO @ Sat, 11 Dec 2021 07:53:23: 16000000 INFO @ Sat, 11 Dec 2021 07:53:25: 12000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:53:27: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:53:27: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:53:27: #1 total tags in treatment: 7553343 INFO @ Sat, 11 Dec 2021 07:53:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:53:27: #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 07:53:27: #1 tags after filtering in treatment: 3844614 INFO @ Sat, 11 Dec 2021 07:53:27: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 11 Dec 2021 07:53:27: #1 finished! INFO @ Sat, 11 Dec 2021 07:53:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:53:27: #2 number of paired peaks: 217 WARNING @ Sat, 11 Dec 2021 07:53:27: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sat, 11 Dec 2021 07:53:27: start model_add_line... INFO @ Sat, 11 Dec 2021 07:53:27: start X-correlation... INFO @ Sat, 11 Dec 2021 07:53:27: end of X-cor INFO @ Sat, 11 Dec 2021 07:53:27: #2 finished! INFO @ Sat, 11 Dec 2021 07:53:27: #2 predicted fragment length is 151 bps INFO @ Sat, 11 Dec 2021 07:53:27: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 11 Dec 2021 07:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.10_model.r WARNING @ Sat, 11 Dec 2021 07:53:27: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:53:27: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sat, 11 Dec 2021 07:53:27: #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 07:53:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:53:32: 13000000 INFO @ Sat, 11 Dec 2021 07:53:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:53:38: 14000000 INFO @ Sat, 11 Dec 2021 07:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.10_summits.bed INFO @ Sat, 11 Dec 2021 07:53:40: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (506 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:53:45: 15000000 INFO @ Sat, 11 Dec 2021 07:53:52: 16000000 INFO @ Sat, 11 Dec 2021 07:53:55: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:53:55: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:53:55: #1 total tags in treatment: 7553343 INFO @ Sat, 11 Dec 2021 07:53:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:53:55: #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 07:53:56: #1 tags after filtering in treatment: 3844614 INFO @ Sat, 11 Dec 2021 07:53:56: #1 Redundant rate of treatment: 0.49 INFO @ Sat, 11 Dec 2021 07:53:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:53:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:53:56: #2 number of paired peaks: 217 WARNING @ Sat, 11 Dec 2021 07:53:56: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Sat, 11 Dec 2021 07:53:56: start model_add_line... INFO @ Sat, 11 Dec 2021 07:53:56: start X-correlation... INFO @ Sat, 11 Dec 2021 07:53:56: end of X-cor INFO @ Sat, 11 Dec 2021 07:53:56: #2 finished! INFO @ Sat, 11 Dec 2021 07:53:56: #2 predicted fragment length is 151 bps INFO @ Sat, 11 Dec 2021 07:53:56: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 11 Dec 2021 07:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.20_model.r WARNING @ Sat, 11 Dec 2021 07:53:56: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:53:56: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sat, 11 Dec 2021 07:53:56: #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 07:53:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:54:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497046/SRX8497046.20_summits.bed INFO @ Sat, 11 Dec 2021 07:54:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 2 millis CompletedMACS2peakCalling