Job ID = 14168299 SRX = SRX9263542 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19792631 spots for SRR12794422/SRR12794422.sra Written 19792631 spots for SRR12794422/SRR12794422.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169464 ("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: 00:39:23 19792631 reads; of these: 19792631 (100.00%) were paired; of these: 13622978 (68.83%) aligned concordantly 0 times 3741739 (18.90%) aligned concordantly exactly 1 time 2427914 (12.27%) aligned concordantly >1 times ---- 13622978 pairs aligned concordantly 0 times; of these: 1661229 (12.19%) aligned discordantly 1 time ---- 11961749 pairs aligned 0 times concordantly or discordantly; of these: 23923498 mates make up the pairs; of these: 21693654 (90.68%) aligned 0 times 463336 (1.94%) aligned exactly 1 time 1766508 (7.38%) aligned >1 times 45.20% overall alignment rate Time searching: 00:39:23 Overall time: 00:39:23 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 16 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] 1093798 / 7757107 = 0.1410 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 @ Fri, 10 Dec 2021 17:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.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 @ Fri, 10 Dec 2021 17:55:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:55:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:56:00: 1000000 INFO @ Fri, 10 Dec 2021 17:56:07: 2000000 INFO @ Fri, 10 Dec 2021 17:56:14: 3000000 INFO @ Fri, 10 Dec 2021 17:56:21: 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 @ Fri, 10 Dec 2021 17:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.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 @ Fri, 10 Dec 2021 17:56:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:56:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:56:28: 5000000 INFO @ Fri, 10 Dec 2021 17:56:32: 1000000 INFO @ Fri, 10 Dec 2021 17:56:36: 6000000 INFO @ Fri, 10 Dec 2021 17:56:41: 2000000 INFO @ Fri, 10 Dec 2021 17:56:44: 7000000 INFO @ Fri, 10 Dec 2021 17:56:50: 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 @ Fri, 10 Dec 2021 17:56:52: 8000000 INFO @ Fri, 10 Dec 2021 17:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.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 @ Fri, 10 Dec 2021 17:56:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:56:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:56:59: 4000000 INFO @ Fri, 10 Dec 2021 17:57:00: 9000000 INFO @ Fri, 10 Dec 2021 17:57:02: 1000000 INFO @ Fri, 10 Dec 2021 17:57:08: 5000000 INFO @ Fri, 10 Dec 2021 17:57:08: 10000000 INFO @ Fri, 10 Dec 2021 17:57:10: 2000000 INFO @ Fri, 10 Dec 2021 17:57:16: 11000000 INFO @ Fri, 10 Dec 2021 17:57:17: 6000000 INFO @ Fri, 10 Dec 2021 17:57:18: 3000000 INFO @ Fri, 10 Dec 2021 17:57:24: 12000000 INFO @ Fri, 10 Dec 2021 17:57:26: 4000000 INFO @ Fri, 10 Dec 2021 17:57:26: 7000000 INFO @ Fri, 10 Dec 2021 17:57:32: 13000000 INFO @ Fri, 10 Dec 2021 17:57:34: 5000000 INFO @ Fri, 10 Dec 2021 17:57:35: 8000000 INFO @ Fri, 10 Dec 2021 17:57:40: 14000000 INFO @ Fri, 10 Dec 2021 17:57:42: 6000000 INFO @ Fri, 10 Dec 2021 17:57:44: 9000000 INFO @ Fri, 10 Dec 2021 17:57:48: 15000000 INFO @ Fri, 10 Dec 2021 17:57:50: 7000000 INFO @ Fri, 10 Dec 2021 17:57:53: 10000000 INFO @ Fri, 10 Dec 2021 17:57:54: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 17:57:54: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 17:57:54: #1 total tags in treatment: 5182682 INFO @ Fri, 10 Dec 2021 17:57:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:57:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:57:54: #1 tags after filtering in treatment: 4391506 INFO @ Fri, 10 Dec 2021 17:57:54: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:57:54: #1 finished! INFO @ Fri, 10 Dec 2021 17:57:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:57:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:57:54: #2 number of paired peaks: 1224 INFO @ Fri, 10 Dec 2021 17:57:54: start model_add_line... INFO @ Fri, 10 Dec 2021 17:57:54: start X-correlation... INFO @ Fri, 10 Dec 2021 17:57:54: end of X-cor INFO @ Fri, 10 Dec 2021 17:57:54: #2 finished! INFO @ Fri, 10 Dec 2021 17:57:54: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 17:57:54: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 17:57:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.05_model.r WARNING @ Fri, 10 Dec 2021 17:57:54: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:57:54: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Fri, 10 Dec 2021 17:57:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:57:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:57:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:57:58: 8000000 INFO @ Fri, 10 Dec 2021 17:58:01: 11000000 INFO @ Fri, 10 Dec 2021 17:58:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:58:05: 9000000 INFO @ Fri, 10 Dec 2021 17:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.05_summits.bed INFO @ Fri, 10 Dec 2021 17:58:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2539 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:58:10: 12000000 INFO @ Fri, 10 Dec 2021 17:58:13: 10000000 INFO @ Fri, 10 Dec 2021 17:58:19: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:58:21: 11000000 INFO @ Fri, 10 Dec 2021 17:58:28: 14000000 INFO @ Fri, 10 Dec 2021 17:58:29: 12000000 INFO @ Fri, 10 Dec 2021 17:58:37: 13000000 INFO @ Fri, 10 Dec 2021 17:58:37: 15000000 INFO @ Fri, 10 Dec 2021 17:58:43: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 17:58:43: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 17:58:43: #1 total tags in treatment: 5182682 INFO @ Fri, 10 Dec 2021 17:58:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:58:43: #1 tags after filtering in treatment: 4391506 INFO @ Fri, 10 Dec 2021 17:58:43: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:58:43: #1 finished! INFO @ Fri, 10 Dec 2021 17:58:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:58:44: #2 number of paired peaks: 1224 INFO @ Fri, 10 Dec 2021 17:58:44: start model_add_line... INFO @ Fri, 10 Dec 2021 17:58:44: start X-correlation... INFO @ Fri, 10 Dec 2021 17:58:44: end of X-cor INFO @ Fri, 10 Dec 2021 17:58:44: #2 finished! INFO @ Fri, 10 Dec 2021 17:58:44: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 17:58:44: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 17:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.10_model.r WARNING @ Fri, 10 Dec 2021 17:58:44: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:58:44: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Fri, 10 Dec 2021 17:58:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:58:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:58:44: 14000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:58:52: 15000000 INFO @ Fri, 10 Dec 2021 17:58:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:58:57: #1 tag size is determined as 126 bps INFO @ Fri, 10 Dec 2021 17:58:57: #1 tag size = 126 INFO @ Fri, 10 Dec 2021 17:58:57: #1 total tags in treatment: 5182682 INFO @ Fri, 10 Dec 2021 17:58:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:58:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 17:58:57: #1 tags after filtering in treatment: 4391506 INFO @ Fri, 10 Dec 2021 17:58:57: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 10 Dec 2021 17:58:57: #1 finished! INFO @ Fri, 10 Dec 2021 17:58:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:58:57: #2 number of paired peaks: 1224 INFO @ Fri, 10 Dec 2021 17:58:57: start model_add_line... INFO @ Fri, 10 Dec 2021 17:58:57: start X-correlation... INFO @ Fri, 10 Dec 2021 17:58:57: end of X-cor INFO @ Fri, 10 Dec 2021 17:58:57: #2 finished! INFO @ Fri, 10 Dec 2021 17:58:57: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Dec 2021 17:58:57: #2 alternative fragment length(s) may be 199 bps INFO @ Fri, 10 Dec 2021 17:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.20_model.r WARNING @ Fri, 10 Dec 2021 17:58:57: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:58:57: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Fri, 10 Dec 2021 17:58:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 17:58:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.10_summits.bed INFO @ Fri, 10 Dec 2021 17:58:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1218 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:59:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:59:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:59:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:59:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9263542/SRX9263542.20_summits.bed INFO @ Fri, 10 Dec 2021 17:59:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling