Job ID = 14170047 SRX = SRX8556249 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 45996494 spots for SRR12024623/SRR12024623.sra Written 45996494 spots for SRR12024623/SRR12024623.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170692 ("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: 00:45:12 45996494 reads; of these: 45996494 (100.00%) were paired; of these: 40278650 (87.57%) aligned concordantly 0 times 3303273 (7.18%) aligned concordantly exactly 1 time 2414571 (5.25%) aligned concordantly >1 times ---- 40278650 pairs aligned concordantly 0 times; of these: 1058894 (2.63%) aligned discordantly 1 time ---- 39219756 pairs aligned 0 times concordantly or discordantly; of these: 78439512 mates make up the pairs; of these: 76049464 (96.95%) aligned 0 times 339269 (0.43%) aligned exactly 1 time 2050779 (2.61%) aligned >1 times 17.33% overall alignment rate Time searching: 00:45:12 Overall time: 00:45:12 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] 1322152 / 6722671 = 0.1967 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 05:51:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.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 05:51:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:51:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:51:17: 1000000 INFO @ Sat, 11 Dec 2021 05:51:25: 2000000 INFO @ Sat, 11 Dec 2021 05:51:33: 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 05:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.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 05:51:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:51:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:51:41: 4000000 INFO @ Sat, 11 Dec 2021 05:51:49: 1000000 INFO @ Sat, 11 Dec 2021 05:51:51: 5000000 INFO @ Sat, 11 Dec 2021 05:51:59: 2000000 INFO @ Sat, 11 Dec 2021 05:52:01: 6000000 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 05:52:09: 3000000 INFO @ Sat, 11 Dec 2021 05:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.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 05:52:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:52:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:52:11: 7000000 INFO @ Sat, 11 Dec 2021 05:52:18: 4000000 INFO @ Sat, 11 Dec 2021 05:52:19: 1000000 INFO @ Sat, 11 Dec 2021 05:52:21: 8000000 INFO @ Sat, 11 Dec 2021 05:52:28: 5000000 INFO @ Sat, 11 Dec 2021 05:52:29: 2000000 INFO @ Sat, 11 Dec 2021 05:52:30: 9000000 INFO @ Sat, 11 Dec 2021 05:52:38: 6000000 INFO @ Sat, 11 Dec 2021 05:52:39: 3000000 INFO @ Sat, 11 Dec 2021 05:52:40: 10000000 INFO @ Sat, 11 Dec 2021 05:52:48: 7000000 INFO @ Sat, 11 Dec 2021 05:52:49: 4000000 INFO @ Sat, 11 Dec 2021 05:52:50: 11000000 INFO @ Sat, 11 Dec 2021 05:52:58: 8000000 INFO @ Sat, 11 Dec 2021 05:52:58: 5000000 INFO @ Sat, 11 Dec 2021 05:53:00: 12000000 INFO @ Sat, 11 Dec 2021 05:53:07: 9000000 INFO @ Sat, 11 Dec 2021 05:53:08: 6000000 INFO @ Sat, 11 Dec 2021 05:53:10: 13000000 INFO @ Sat, 11 Dec 2021 05:53:13: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:53:13: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:53:13: #1 total tags in treatment: 4470737 INFO @ Sat, 11 Dec 2021 05:53:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:53:13: #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 05:53:13: #1 tags after filtering in treatment: 3773904 INFO @ Sat, 11 Dec 2021 05:53:13: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 05:53:13: #1 finished! INFO @ Sat, 11 Dec 2021 05:53:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:53:13: #2 number of paired peaks: 493 WARNING @ Sat, 11 Dec 2021 05:53:13: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 11 Dec 2021 05:53:13: start model_add_line... INFO @ Sat, 11 Dec 2021 05:53:13: start X-correlation... INFO @ Sat, 11 Dec 2021 05:53:13: end of X-cor INFO @ Sat, 11 Dec 2021 05:53:13: #2 finished! INFO @ Sat, 11 Dec 2021 05:53:13: #2 predicted fragment length is 191 bps INFO @ Sat, 11 Dec 2021 05:53:13: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 11 Dec 2021 05:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.05_model.r WARNING @ Sat, 11 Dec 2021 05:53:13: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:53:13: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 11 Dec 2021 05:53:13: #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 05:53:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:53:16: 10000000 INFO @ Sat, 11 Dec 2021 05:53:18: 7000000 INFO @ Sat, 11 Dec 2021 05:53:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 05:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.05_peaks.xls INFO @ Sat, 11 Dec 2021 05:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.05_summits.bed INFO @ Sat, 11 Dec 2021 05:53:26: Done! INFO @ Sat, 11 Dec 2021 05:53:26: 11000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 05:53:28: 8000000 INFO @ Sat, 11 Dec 2021 05:53:36: 12000000 INFO @ Sat, 11 Dec 2021 05:53:37: 9000000 INFO @ Sat, 11 Dec 2021 05:53:46: 13000000 INFO @ Sat, 11 Dec 2021 05:53:47: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 05:53:49: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:53:49: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:53:49: #1 total tags in treatment: 4470737 INFO @ Sat, 11 Dec 2021 05:53:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:53:49: #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 05:53:49: #1 tags after filtering in treatment: 3773904 INFO @ Sat, 11 Dec 2021 05:53:49: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 05:53:49: #1 finished! INFO @ Sat, 11 Dec 2021 05:53:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:53:49: #2 number of paired peaks: 493 WARNING @ Sat, 11 Dec 2021 05:53:49: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 11 Dec 2021 05:53:49: start model_add_line... INFO @ Sat, 11 Dec 2021 05:53:49: start X-correlation... INFO @ Sat, 11 Dec 2021 05:53:49: end of X-cor INFO @ Sat, 11 Dec 2021 05:53:49: #2 finished! INFO @ Sat, 11 Dec 2021 05:53:49: #2 predicted fragment length is 191 bps INFO @ Sat, 11 Dec 2021 05:53:49: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 11 Dec 2021 05:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.10_model.r WARNING @ Sat, 11 Dec 2021 05:53:49: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:53:49: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 11 Dec 2021 05:53:49: #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 05:53:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:53:56: 11000000 INFO @ Sat, 11 Dec 2021 05:53:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.10_peaks.xls INFO @ Sat, 11 Dec 2021 05:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.10_summits.bed INFO @ Sat, 11 Dec 2021 05:54:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (643 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 05:54:05: 12000000 INFO @ Sat, 11 Dec 2021 05:54:14: 13000000 INFO @ Sat, 11 Dec 2021 05:54:16: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:54:16: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:54:16: #1 total tags in treatment: 4470737 INFO @ Sat, 11 Dec 2021 05:54:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:54:16: #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 05:54:16: #1 tags after filtering in treatment: 3773904 INFO @ Sat, 11 Dec 2021 05:54:16: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 05:54:16: #1 finished! INFO @ Sat, 11 Dec 2021 05:54:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:54:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:54:16: #2 number of paired peaks: 493 WARNING @ Sat, 11 Dec 2021 05:54:16: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 11 Dec 2021 05:54:16: start model_add_line... INFO @ Sat, 11 Dec 2021 05:54:17: start X-correlation... INFO @ Sat, 11 Dec 2021 05:54:17: end of X-cor INFO @ Sat, 11 Dec 2021 05:54:17: #2 finished! INFO @ Sat, 11 Dec 2021 05:54:17: #2 predicted fragment length is 191 bps INFO @ Sat, 11 Dec 2021 05:54:17: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 11 Dec 2021 05:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.20_model.r WARNING @ Sat, 11 Dec 2021 05:54:17: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:54:17: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 11 Dec 2021 05:54:17: #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 05:54:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:54:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.20_peaks.xls INFO @ Sat, 11 Dec 2021 05:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556249/SRX8556249.20_summits.bed INFO @ Sat, 11 Dec 2021 05:54:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 1 millis CompletedMACS2peakCalling