Job ID = 14170116 SRX = SRX8556373 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19675544 spots for SRR12024929/SRR12024929.sra Written 19675544 spots for SRR12024929/SRR12024929.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170740 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:46:05 19675544 reads; of these: 19675544 (100.00%) were paired; of these: 9757312 (49.59%) aligned concordantly 0 times 7059268 (35.88%) aligned concordantly exactly 1 time 2858964 (14.53%) aligned concordantly >1 times ---- 9757312 pairs aligned concordantly 0 times; of these: 2424648 (24.85%) aligned discordantly 1 time ---- 7332664 pairs aligned 0 times concordantly or discordantly; of these: 14665328 mates make up the pairs; of these: 12409179 (84.62%) aligned 0 times 435165 (2.97%) aligned exactly 1 time 1820984 (12.42%) aligned >1 times 68.47% overall alignment rate Time searching: 00:46:06 Overall time: 00:46:06 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 20 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] 3228970 / 12192320 = 0.2648 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 06:30:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.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 06:30:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:30:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:30:22: 1000000 INFO @ Sat, 11 Dec 2021 06:30:33: 2000000 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 06:30:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.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 06:30:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:30:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:30:43: 3000000 INFO @ Sat, 11 Dec 2021 06:30:54: 1000000 INFO @ Sat, 11 Dec 2021 06:30:54: 4000000 INFO @ Sat, 11 Dec 2021 06:31:05: 2000000 INFO @ Sat, 11 Dec 2021 06:31:06: 5000000 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 06:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.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 06:31:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:31:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:31:16: 3000000 INFO @ Sat, 11 Dec 2021 06:31:17: 6000000 INFO @ Sat, 11 Dec 2021 06:31:22: 1000000 INFO @ Sat, 11 Dec 2021 06:31:28: 4000000 INFO @ Sat, 11 Dec 2021 06:31:28: 7000000 INFO @ Sat, 11 Dec 2021 06:31:32: 2000000 INFO @ Sat, 11 Dec 2021 06:31:39: 5000000 INFO @ Sat, 11 Dec 2021 06:31:40: 8000000 INFO @ Sat, 11 Dec 2021 06:31:42: 3000000 INFO @ Sat, 11 Dec 2021 06:31:50: 6000000 INFO @ Sat, 11 Dec 2021 06:31:51: 9000000 INFO @ Sat, 11 Dec 2021 06:31:52: 4000000 INFO @ Sat, 11 Dec 2021 06:32:01: 5000000 INFO @ Sat, 11 Dec 2021 06:32:02: 7000000 INFO @ Sat, 11 Dec 2021 06:32:02: 10000000 INFO @ Sat, 11 Dec 2021 06:32:11: 6000000 INFO @ Sat, 11 Dec 2021 06:32:13: 8000000 INFO @ Sat, 11 Dec 2021 06:32:13: 11000000 INFO @ Sat, 11 Dec 2021 06:32:21: 7000000 INFO @ Sat, 11 Dec 2021 06:32:24: 9000000 INFO @ Sat, 11 Dec 2021 06:32:25: 12000000 INFO @ Sat, 11 Dec 2021 06:32:31: 8000000 INFO @ Sat, 11 Dec 2021 06:32:36: 13000000 INFO @ Sat, 11 Dec 2021 06:32:36: 10000000 INFO @ Sat, 11 Dec 2021 06:32:40: 9000000 INFO @ Sat, 11 Dec 2021 06:32:46: 14000000 INFO @ Sat, 11 Dec 2021 06:32:47: 11000000 INFO @ Sat, 11 Dec 2021 06:32:50: 10000000 INFO @ Sat, 11 Dec 2021 06:32:57: 15000000 INFO @ Sat, 11 Dec 2021 06:32:58: 12000000 INFO @ Sat, 11 Dec 2021 06:33:00: 11000000 INFO @ Sat, 11 Dec 2021 06:33:08: 16000000 INFO @ Sat, 11 Dec 2021 06:33:09: 13000000 INFO @ Sat, 11 Dec 2021 06:33:09: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:33:19: 13000000 INFO @ Sat, 11 Dec 2021 06:33:19: 17000000 INFO @ Sat, 11 Dec 2021 06:33:20: 14000000 INFO @ Sat, 11 Dec 2021 06:33:28: 14000000 INFO @ Sat, 11 Dec 2021 06:33:30: 18000000 INFO @ Sat, 11 Dec 2021 06:33:31: 15000000 INFO @ Sat, 11 Dec 2021 06:33:38: 15000000 INFO @ Sat, 11 Dec 2021 06:33:41: 19000000 INFO @ Sat, 11 Dec 2021 06:33:42: 16000000 INFO @ Sat, 11 Dec 2021 06:33:48: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:33:52: 20000000 INFO @ Sat, 11 Dec 2021 06:33:53: 17000000 INFO @ Sat, 11 Dec 2021 06:33:57: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:33:57: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:33:57: #1 total tags in treatment: 7162860 INFO @ Sat, 11 Dec 2021 06:33:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:33:57: #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 06:33:57: #1 tags after filtering in treatment: 6694611 INFO @ Sat, 11 Dec 2021 06:33:57: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 06:33:57: #1 finished! INFO @ Sat, 11 Dec 2021 06:33:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:33:57: 17000000 INFO @ Sat, 11 Dec 2021 06:33:58: #2 number of paired peaks: 282 WARNING @ Sat, 11 Dec 2021 06:33:58: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 11 Dec 2021 06:33:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:33:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:33:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:33:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:33:58: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Dec 2021 06:33:58: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Dec 2021 06:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.05_model.r WARNING @ Sat, 11 Dec 2021 06:33:58: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:33:58: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sat, 11 Dec 2021 06:33:58: #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 06:33:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:34:04: 18000000 INFO @ Sat, 11 Dec 2021 06:34:07: 18000000 INFO @ Sat, 11 Dec 2021 06:34:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:34:15: 19000000 INFO @ Sat, 11 Dec 2021 06:34:17: 19000000 INFO @ Sat, 11 Dec 2021 06:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.05_summits.bed INFO @ Sat, 11 Dec 2021 06:34:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1833 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:34:25: 20000000 INFO @ Sat, 11 Dec 2021 06:34:26: 20000000 INFO @ Sat, 11 Dec 2021 06:34:30: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:34:30: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:34:30: #1 total tags in treatment: 7162860 INFO @ Sat, 11 Dec 2021 06:34:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:34:30: #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 06:34:30: #1 tags after filtering in treatment: 6694611 INFO @ Sat, 11 Dec 2021 06:34:30: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 06:34:30: #1 finished! INFO @ Sat, 11 Dec 2021 06:34:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:34:31: #2 number of paired peaks: 282 WARNING @ Sat, 11 Dec 2021 06:34:31: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 11 Dec 2021 06:34:31: start model_add_line... INFO @ Sat, 11 Dec 2021 06:34:31: start X-correlation... INFO @ Sat, 11 Dec 2021 06:34:31: end of X-cor INFO @ Sat, 11 Dec 2021 06:34:31: #2 finished! INFO @ Sat, 11 Dec 2021 06:34:31: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Dec 2021 06:34:31: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Dec 2021 06:34:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.10_model.r WARNING @ Sat, 11 Dec 2021 06:34:31: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:34:31: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sat, 11 Dec 2021 06:34:31: #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 06:34:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:34:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:34:31: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:34:31: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:34:31: #1 total tags in treatment: 7162860 INFO @ Sat, 11 Dec 2021 06:34:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:34:31: #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 06:34:31: #1 tags after filtering in treatment: 6694611 INFO @ Sat, 11 Dec 2021 06:34:31: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 11 Dec 2021 06:34:31: #1 finished! INFO @ Sat, 11 Dec 2021 06:34:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:34:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:34:32: #2 number of paired peaks: 282 WARNING @ Sat, 11 Dec 2021 06:34:32: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 11 Dec 2021 06:34:32: start model_add_line... INFO @ Sat, 11 Dec 2021 06:34:32: start X-correlation... INFO @ Sat, 11 Dec 2021 06:34:32: end of X-cor INFO @ Sat, 11 Dec 2021 06:34:32: #2 finished! INFO @ Sat, 11 Dec 2021 06:34:32: #2 predicted fragment length is 182 bps INFO @ Sat, 11 Dec 2021 06:34:32: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 11 Dec 2021 06:34:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.20_model.r WARNING @ Sat, 11 Dec 2021 06:34:32: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:34:32: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Sat, 11 Dec 2021 06:34:32: #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 06:34:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:34:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:34:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:34:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:34:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.10_summits.bed INFO @ Sat, 11 Dec 2021 06:34:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (820 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556373/SRX8556373.20_summits.bed INFO @ Sat, 11 Dec 2021 06:34:52: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 4 millis CompletedMACS2peakCalling