Job ID = 12265179 SRX = SRX3282113 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19383698 spots for SRR6171264/SRR6171264.sra Written 19383698 spots for SRR6171264/SRR6171264.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265521 ("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: 00:42:19 19383698 reads; of these: 19383698 (100.00%) were paired; of these: 7414730 (38.25%) aligned concordantly 0 times 3672144 (18.94%) aligned concordantly exactly 1 time 8296824 (42.80%) aligned concordantly >1 times ---- 7414730 pairs aligned concordantly 0 times; of these: 677835 (9.14%) aligned discordantly 1 time ---- 6736895 pairs aligned 0 times concordantly or discordantly; of these: 13473790 mates make up the pairs; of these: 10254030 (76.10%) aligned 0 times 255768 (1.90%) aligned exactly 1 time 2963992 (22.00%) aligned >1 times 73.55% overall alignment rate Time searching: 00:42:19 Overall time: 00:42:19 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] 6388504 / 12554642 = 0.5089 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 07:07:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.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 07:07:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:38: 1000000 INFO @ Sat, 03 Apr 2021 07:07:45: 2000000 INFO @ Sat, 03 Apr 2021 07:07:53: 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 07:08:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.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 07:08:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:08:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:08:01: 4000000 INFO @ Sat, 03 Apr 2021 07:08:09: 5000000 INFO @ Sat, 03 Apr 2021 07:08:09: 1000000 INFO @ Sat, 03 Apr 2021 07:08:17: 6000000 INFO @ Sat, 03 Apr 2021 07:08:18: 2000000 INFO @ Sat, 03 Apr 2021 07:08:25: 7000000 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 07:08:28: 3000000 INFO @ Sat, 03 Apr 2021 07:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.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 07:08:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:08:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:08:32: 8000000 INFO @ Sat, 03 Apr 2021 07:08:38: 4000000 INFO @ Sat, 03 Apr 2021 07:08:39: 9000000 INFO @ Sat, 03 Apr 2021 07:08:39: 1000000 INFO @ Sat, 03 Apr 2021 07:08:46: 10000000 INFO @ Sat, 03 Apr 2021 07:08:47: 5000000 INFO @ Sat, 03 Apr 2021 07:08:49: 2000000 INFO @ Sat, 03 Apr 2021 07:08:53: 11000000 INFO @ Sat, 03 Apr 2021 07:08:57: 6000000 INFO @ Sat, 03 Apr 2021 07:08:58: 3000000 INFO @ Sat, 03 Apr 2021 07:09:00: 12000000 INFO @ Sat, 03 Apr 2021 07:09:07: 7000000 INFO @ Sat, 03 Apr 2021 07:09:07: 4000000 INFO @ Sat, 03 Apr 2021 07:09:07: 13000000 INFO @ Sat, 03 Apr 2021 07:09:16: 14000000 INFO @ Sat, 03 Apr 2021 07:09:16: 8000000 INFO @ Sat, 03 Apr 2021 07:09:17: 5000000 INFO @ Sat, 03 Apr 2021 07:09:23: 15000000 INFO @ Sat, 03 Apr 2021 07:09:25: 9000000 INFO @ Sat, 03 Apr 2021 07:09:26: 6000000 INFO @ Sat, 03 Apr 2021 07:09:29: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 07:09:29: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 07:09:29: #1 total tags in treatment: 5647980 INFO @ Sat, 03 Apr 2021 07:09:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:09:29: #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 07:09:29: #1 tags after filtering in treatment: 4124345 INFO @ Sat, 03 Apr 2021 07:09:29: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:09:29: #1 finished! INFO @ Sat, 03 Apr 2021 07:09:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:09:30: #2 number of paired peaks: 594 WARNING @ Sat, 03 Apr 2021 07:09:30: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 03 Apr 2021 07:09:30: start model_add_line... INFO @ Sat, 03 Apr 2021 07:09:30: start X-correlation... INFO @ Sat, 03 Apr 2021 07:09:30: end of X-cor INFO @ Sat, 03 Apr 2021 07:09:30: #2 finished! INFO @ Sat, 03 Apr 2021 07:09:30: #2 predicted fragment length is 152 bps INFO @ Sat, 03 Apr 2021 07:09:30: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 03 Apr 2021 07:09:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.05_model.r WARNING @ Sat, 03 Apr 2021 07:09:30: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:09:30: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Sat, 03 Apr 2021 07:09:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:09:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:09:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:09:33: 10000000 INFO @ Sat, 03 Apr 2021 07:09:35: 7000000 INFO @ Sat, 03 Apr 2021 07:09:42: 11000000 INFO @ Sat, 03 Apr 2021 07:09:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:09:44: 8000000 INFO @ Sat, 03 Apr 2021 07:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.05_summits.bed INFO @ Sat, 03 Apr 2021 07:09:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2292 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:09:50: 12000000 INFO @ Sat, 03 Apr 2021 07:09:52: 9000000 INFO @ Sat, 03 Apr 2021 07:09:58: 13000000 INFO @ Sat, 03 Apr 2021 07:10:00: 10000000 INFO @ Sat, 03 Apr 2021 07:10:07: 14000000 INFO @ Sat, 03 Apr 2021 07:10:08: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:10:16: 12000000 INFO @ Sat, 03 Apr 2021 07:10:16: 15000000 INFO @ Sat, 03 Apr 2021 07:10:22: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 07:10:22: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 07:10:22: #1 total tags in treatment: 5647980 INFO @ Sat, 03 Apr 2021 07:10:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:10:22: #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 07:10:22: #1 tags after filtering in treatment: 4124345 INFO @ Sat, 03 Apr 2021 07:10:22: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:10:22: #1 finished! INFO @ Sat, 03 Apr 2021 07:10:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:10:23: #2 number of paired peaks: 594 WARNING @ Sat, 03 Apr 2021 07:10:23: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 03 Apr 2021 07:10:23: start model_add_line... INFO @ Sat, 03 Apr 2021 07:10:23: start X-correlation... INFO @ Sat, 03 Apr 2021 07:10:23: end of X-cor INFO @ Sat, 03 Apr 2021 07:10:23: #2 finished! INFO @ Sat, 03 Apr 2021 07:10:23: #2 predicted fragment length is 152 bps INFO @ Sat, 03 Apr 2021 07:10:23: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 03 Apr 2021 07:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.10_model.r WARNING @ Sat, 03 Apr 2021 07:10:23: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:10:23: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Sat, 03 Apr 2021 07:10:23: #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 07:10:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:10:24: 13000000 INFO @ Sat, 03 Apr 2021 07:10:32: 14000000 INFO @ Sat, 03 Apr 2021 07:10:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:10:41: 15000000 INFO @ Sat, 03 Apr 2021 07:10:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:10:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:10:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.10_summits.bed INFO @ Sat, 03 Apr 2021 07:10:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1109 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:10:47: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 07:10:47: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 07:10:47: #1 total tags in treatment: 5647980 INFO @ Sat, 03 Apr 2021 07:10:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:10:47: #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 07:10:47: #1 tags after filtering in treatment: 4124345 INFO @ Sat, 03 Apr 2021 07:10:47: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 07:10:47: #1 finished! INFO @ Sat, 03 Apr 2021 07:10:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:10:47: #2 number of paired peaks: 594 WARNING @ Sat, 03 Apr 2021 07:10:47: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Sat, 03 Apr 2021 07:10:47: start model_add_line... INFO @ Sat, 03 Apr 2021 07:10:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:10:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:10:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:10:47: #2 predicted fragment length is 152 bps INFO @ Sat, 03 Apr 2021 07:10:47: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 03 Apr 2021 07:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.20_model.r WARNING @ Sat, 03 Apr 2021 07:10:47: #2 Since the d (152) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:10:47: #2 You may need to consider one of the other alternative d(s): 152 WARNING @ Sat, 03 Apr 2021 07:10:47: #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 07:10:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:11:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282113/SRX3282113.20_summits.bed INFO @ Sat, 03 Apr 2021 07:11:08: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 3 millis CompletedMACS2peakCalling