Job ID = 12265325 SRX = SRX5736454 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21977685 spots for SRR8956865/SRR8956865.sra Written 21977685 spots for SRR8956865/SRR8956865.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265533 ("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: 00:19:50 21977685 reads; of these: 21977685 (100.00%) were paired; of these: 12728555 (57.92%) aligned concordantly 0 times 2606008 (11.86%) aligned concordantly exactly 1 time 6643122 (30.23%) aligned concordantly >1 times ---- 12728555 pairs aligned concordantly 0 times; of these: 277089 (2.18%) aligned discordantly 1 time ---- 12451466 pairs aligned 0 times concordantly or discordantly; of these: 24902932 mates make up the pairs; of these: 23479803 (94.29%) aligned 0 times 145904 (0.59%) aligned exactly 1 time 1277225 (5.13%) aligned >1 times 46.58% overall alignment rate Time searching: 00:19:50 Overall time: 00:19:50 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 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] 4986937 / 9448909 = 0.5278 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:03:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.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, 03 Apr 2021 07:03:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:03:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:03:43: 1000000 INFO @ Sat, 03 Apr 2021 07:03:50: 2000000 INFO @ Sat, 03 Apr 2021 07:03:57: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:04:05: 4000000 INFO @ Sat, 03 Apr 2021 07:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.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, 03 Apr 2021 07:04:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:04:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:04:12: 1000000 INFO @ Sat, 03 Apr 2021 07:04:13: 5000000 INFO @ Sat, 03 Apr 2021 07:04:19: 2000000 INFO @ Sat, 03 Apr 2021 07:04:20: 6000000 INFO @ Sat, 03 Apr 2021 07:04:26: 3000000 INFO @ Sat, 03 Apr 2021 07:04:27: 7000000 INFO @ Sat, 03 Apr 2021 07:04:33: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:04:34: 8000000 INFO @ Sat, 03 Apr 2021 07:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.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, 03 Apr 2021 07:04:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:04:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:04:40: 5000000 INFO @ Sat, 03 Apr 2021 07:04:42: 9000000 INFO @ Sat, 03 Apr 2021 07:04:43: 1000000 INFO @ Sat, 03 Apr 2021 07:04:46: 6000000 INFO @ Sat, 03 Apr 2021 07:04:50: 2000000 INFO @ Sat, 03 Apr 2021 07:04:50: 10000000 INFO @ Sat, 03 Apr 2021 07:04:52: 7000000 INFO @ Sat, 03 Apr 2021 07:04:54: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:04:54: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:04:54: #1 total tags in treatment: 4288036 INFO @ Sat, 03 Apr 2021 07:04:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:04:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:04:54: #1 tags after filtering in treatment: 3110140 INFO @ Sat, 03 Apr 2021 07:04:54: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:04:54: #1 finished! INFO @ Sat, 03 Apr 2021 07:04:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:04:54: #2 number of paired peaks: 717 WARNING @ Sat, 03 Apr 2021 07:04:54: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Sat, 03 Apr 2021 07:04:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:04:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:04:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:04:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:04:54: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Apr 2021 07:04:54: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Apr 2021 07:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.05_model.r WARNING @ Sat, 03 Apr 2021 07:04:54: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:04:54: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 03 Apr 2021 07:04:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:04:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:04:57: 3000000 INFO @ Sat, 03 Apr 2021 07:04:59: 8000000 INFO @ Sat, 03 Apr 2021 07:05:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:05:03: 4000000 INFO @ Sat, 03 Apr 2021 07:05:05: 9000000 INFO @ Sat, 03 Apr 2021 07:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.05_summits.bed INFO @ Sat, 03 Apr 2021 07:05:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1775 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:05:10: 5000000 INFO @ Sat, 03 Apr 2021 07:05:12: 10000000 INFO @ Sat, 03 Apr 2021 07:05:16: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:05:16: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:05:16: #1 total tags in treatment: 4288036 INFO @ Sat, 03 Apr 2021 07:05:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:05:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:05:16: #1 tags after filtering in treatment: 3110140 INFO @ Sat, 03 Apr 2021 07:05:16: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:05:16: #1 finished! INFO @ Sat, 03 Apr 2021 07:05:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:05:16: #2 number of paired peaks: 717 WARNING @ Sat, 03 Apr 2021 07:05:16: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Sat, 03 Apr 2021 07:05:16: start model_add_line... INFO @ Sat, 03 Apr 2021 07:05:16: start X-correlation... INFO @ Sat, 03 Apr 2021 07:05:16: end of X-cor INFO @ Sat, 03 Apr 2021 07:05:16: #2 finished! INFO @ Sat, 03 Apr 2021 07:05:16: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Apr 2021 07:05:16: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Apr 2021 07:05:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.10_model.r WARNING @ Sat, 03 Apr 2021 07:05:16: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:05:16: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 03 Apr 2021 07:05:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:05:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:05:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:05:16: 6000000 INFO @ Sat, 03 Apr 2021 07:05:22: 7000000 INFO @ Sat, 03 Apr 2021 07:05:24: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:05:28: 8000000 INFO @ Sat, 03 Apr 2021 07:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.10_summits.bed INFO @ Sat, 03 Apr 2021 07:05:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (797 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:05:34: 9000000 INFO @ Sat, 03 Apr 2021 07:05:41: 10000000 INFO @ Sat, 03 Apr 2021 07:05:44: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:05:44: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:05:44: #1 total tags in treatment: 4288036 INFO @ Sat, 03 Apr 2021 07:05:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:05:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:05:44: #1 tags after filtering in treatment: 3110140 INFO @ Sat, 03 Apr 2021 07:05:44: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:05:44: #1 finished! INFO @ Sat, 03 Apr 2021 07:05:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:05:44: #2 number of paired peaks: 717 WARNING @ Sat, 03 Apr 2021 07:05:44: Fewer paired peaks (717) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 717 pairs to build model! INFO @ Sat, 03 Apr 2021 07:05:44: start model_add_line... INFO @ Sat, 03 Apr 2021 07:05:44: start X-correlation... INFO @ Sat, 03 Apr 2021 07:05:44: end of X-cor INFO @ Sat, 03 Apr 2021 07:05:44: #2 finished! INFO @ Sat, 03 Apr 2021 07:05:44: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Apr 2021 07:05:44: #2 alternative fragment length(s) may be 132 bps INFO @ Sat, 03 Apr 2021 07:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.20_model.r WARNING @ Sat, 03 Apr 2021 07:05:44: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:05:44: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sat, 03 Apr 2021 07:05:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:05:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:05:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:05:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:05:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:05:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:05:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736454/SRX5736454.20_summits.bed INFO @ Sat, 03 Apr 2021 07:05:56: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling