Job ID = 14170265 SRX = SRX8556389 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22962091 spots for SRR12024945/SRR12024945.sra Written 22962091 spots for SRR12024945/SRR12024945.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170786 ("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: 00:40:16 22962091 reads; of these: 22962091 (100.00%) were paired; of these: 19521531 (85.02%) aligned concordantly 0 times 1222185 (5.32%) aligned concordantly exactly 1 time 2218375 (9.66%) aligned concordantly >1 times ---- 19521531 pairs aligned concordantly 0 times; of these: 370504 (1.90%) aligned discordantly 1 time ---- 19151027 pairs aligned 0 times concordantly or discordantly; of these: 38302054 mates make up the pairs; of these: 35176441 (91.84%) aligned 0 times 652878 (1.70%) aligned exactly 1 time 2472735 (6.46%) aligned >1 times 23.40% overall alignment rate Time searching: 00:40:16 Overall time: 00:40:16 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] 2169432 / 3720196 = 0.5831 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 06:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.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 06:43:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:43:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:43:54: 1000000 INFO @ Sat, 11 Dec 2021 06:44:00: 2000000 INFO @ Sat, 11 Dec 2021 06:44:07: 3000000 INFO @ Sat, 11 Dec 2021 06:44:13: 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 @ Sat, 11 Dec 2021 06:44:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.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 06:44:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:20: 5000000 INFO @ Sat, 11 Dec 2021 06:44:25: 1000000 INFO @ Sat, 11 Dec 2021 06:44:27: 6000000 INFO @ Sat, 11 Dec 2021 06:44:30: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:44:30: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:44:30: #1 total tags in treatment: 1424783 INFO @ Sat, 11 Dec 2021 06:44:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:44:30: #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 06:44:30: #1 tags after filtering in treatment: 835655 INFO @ Sat, 11 Dec 2021 06:44:30: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 11 Dec 2021 06:44:30: #1 finished! INFO @ Sat, 11 Dec 2021 06:44:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:44:30: #2 number of paired peaks: 1022 INFO @ Sat, 11 Dec 2021 06:44:30: start model_add_line... INFO @ Sat, 11 Dec 2021 06:44:30: start X-correlation... INFO @ Sat, 11 Dec 2021 06:44:30: end of X-cor INFO @ Sat, 11 Dec 2021 06:44:30: #2 finished! INFO @ Sat, 11 Dec 2021 06:44:30: #2 predicted fragment length is 164 bps INFO @ Sat, 11 Dec 2021 06:44:30: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 11 Dec 2021 06:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.05_model.r WARNING @ Sat, 11 Dec 2021 06:44:30: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:44:30: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Sat, 11 Dec 2021 06:44:30: #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 06:44:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:44:32: 2000000 INFO @ Sat, 11 Dec 2021 06:44:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.05_summits.bed INFO @ Sat, 11 Dec 2021 06:44:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (907 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:44:39: 3000000 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 06:44:46: 4000000 INFO @ Sat, 11 Dec 2021 06:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.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 06:44:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:53: 5000000 INFO @ Sat, 11 Dec 2021 06:44:54: 1000000 INFO @ Sat, 11 Dec 2021 06:45:00: 6000000 INFO @ Sat, 11 Dec 2021 06:45:00: 2000000 INFO @ Sat, 11 Dec 2021 06:45:03: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:45:03: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:45:03: #1 total tags in treatment: 1424783 INFO @ Sat, 11 Dec 2021 06:45:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:45:03: #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 06:45:03: #1 tags after filtering in treatment: 835655 INFO @ Sat, 11 Dec 2021 06:45:03: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 11 Dec 2021 06:45:03: #1 finished! INFO @ Sat, 11 Dec 2021 06:45:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:45:03: #2 number of paired peaks: 1022 INFO @ Sat, 11 Dec 2021 06:45:03: start model_add_line... INFO @ Sat, 11 Dec 2021 06:45:03: start X-correlation... INFO @ Sat, 11 Dec 2021 06:45:03: end of X-cor INFO @ Sat, 11 Dec 2021 06:45:03: #2 finished! INFO @ Sat, 11 Dec 2021 06:45:03: #2 predicted fragment length is 164 bps INFO @ Sat, 11 Dec 2021 06:45:03: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 11 Dec 2021 06:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.10_model.r WARNING @ Sat, 11 Dec 2021 06:45:03: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:45:03: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Sat, 11 Dec 2021 06:45:03: #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 06:45:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:45:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.10_summits.bed INFO @ Sat, 11 Dec 2021 06:45:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (694 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:45:07: 3000000 INFO @ Sat, 11 Dec 2021 06:45:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:45:20: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:45:27: 6000000 INFO @ Sat, 11 Dec 2021 06:45:30: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:45:30: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:45:30: #1 total tags in treatment: 1424783 INFO @ Sat, 11 Dec 2021 06:45:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:45:30: #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 06:45:30: #1 tags after filtering in treatment: 835655 INFO @ Sat, 11 Dec 2021 06:45:30: #1 Redundant rate of treatment: 0.41 INFO @ Sat, 11 Dec 2021 06:45:30: #1 finished! INFO @ Sat, 11 Dec 2021 06:45:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:45:30: #2 number of paired peaks: 1022 INFO @ Sat, 11 Dec 2021 06:45:30: start model_add_line... INFO @ Sat, 11 Dec 2021 06:45:30: start X-correlation... INFO @ Sat, 11 Dec 2021 06:45:30: end of X-cor INFO @ Sat, 11 Dec 2021 06:45:30: #2 finished! INFO @ Sat, 11 Dec 2021 06:45:30: #2 predicted fragment length is 164 bps INFO @ Sat, 11 Dec 2021 06:45:30: #2 alternative fragment length(s) may be 164 bps INFO @ Sat, 11 Dec 2021 06:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.20_model.r WARNING @ Sat, 11 Dec 2021 06:45:30: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:45:30: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Sat, 11 Dec 2021 06:45:30: #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 06:45:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:45:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556389/SRX8556389.20_summits.bed INFO @ Sat, 11 Dec 2021 06:45:33: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (481 records, 4 fields): 2 millis CompletedMACS2peakCalling