Job ID = 14167408 SRX = SRX8574269 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:19 52941533 reads; of these: 52941533 (100.00%) were unpaired; of these: 15179314 (28.67%) aligned 0 times 25624754 (48.40%) aligned exactly 1 time 12137465 (22.93%) aligned >1 times 71.33% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 14382366 / 37762219 = 0.3809 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 12:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.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 12:28:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:28:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:28:29: 1000000 INFO @ Fri, 10 Dec 2021 12:28:35: 2000000 INFO @ Fri, 10 Dec 2021 12:28:41: 3000000 INFO @ Fri, 10 Dec 2021 12:28:47: 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 12:28:53: 5000000 INFO @ Fri, 10 Dec 2021 12:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.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 12:28:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:28:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:28:59: 1000000 INFO @ Fri, 10 Dec 2021 12:28:59: 6000000 INFO @ Fri, 10 Dec 2021 12:29:04: 2000000 INFO @ Fri, 10 Dec 2021 12:29:06: 7000000 INFO @ Fri, 10 Dec 2021 12:29:10: 3000000 INFO @ Fri, 10 Dec 2021 12:29:13: 8000000 INFO @ Fri, 10 Dec 2021 12:29:16: 4000000 INFO @ Fri, 10 Dec 2021 12:29:19: 9000000 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 12:29:22: 5000000 INFO @ Fri, 10 Dec 2021 12:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.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 12:29:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:29:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:29:26: 10000000 INFO @ Fri, 10 Dec 2021 12:29:28: 6000000 INFO @ Fri, 10 Dec 2021 12:29:29: 1000000 INFO @ Fri, 10 Dec 2021 12:29:32: 11000000 INFO @ Fri, 10 Dec 2021 12:29:33: 7000000 INFO @ Fri, 10 Dec 2021 12:29:34: 2000000 INFO @ Fri, 10 Dec 2021 12:29:39: 12000000 INFO @ Fri, 10 Dec 2021 12:29:39: 8000000 INFO @ Fri, 10 Dec 2021 12:29:40: 3000000 INFO @ Fri, 10 Dec 2021 12:29:45: 9000000 INFO @ Fri, 10 Dec 2021 12:29:45: 13000000 INFO @ Fri, 10 Dec 2021 12:29:46: 4000000 INFO @ Fri, 10 Dec 2021 12:29:51: 10000000 INFO @ Fri, 10 Dec 2021 12:29:51: 14000000 INFO @ Fri, 10 Dec 2021 12:29:52: 5000000 INFO @ Fri, 10 Dec 2021 12:29:56: 11000000 INFO @ Fri, 10 Dec 2021 12:29:58: 6000000 INFO @ Fri, 10 Dec 2021 12:29:58: 15000000 INFO @ Fri, 10 Dec 2021 12:30:02: 12000000 INFO @ Fri, 10 Dec 2021 12:30:03: 7000000 INFO @ Fri, 10 Dec 2021 12:30:04: 16000000 INFO @ Fri, 10 Dec 2021 12:30:08: 13000000 INFO @ Fri, 10 Dec 2021 12:30:09: 8000000 INFO @ Fri, 10 Dec 2021 12:30:11: 17000000 INFO @ Fri, 10 Dec 2021 12:30:14: 14000000 INFO @ Fri, 10 Dec 2021 12:30:15: 9000000 INFO @ Fri, 10 Dec 2021 12:30:18: 18000000 INFO @ Fri, 10 Dec 2021 12:30:20: 15000000 INFO @ Fri, 10 Dec 2021 12:30:21: 10000000 INFO @ Fri, 10 Dec 2021 12:30:25: 19000000 INFO @ Fri, 10 Dec 2021 12:30:26: 16000000 INFO @ Fri, 10 Dec 2021 12:30:26: 11000000 INFO @ Fri, 10 Dec 2021 12:30:31: 20000000 INFO @ Fri, 10 Dec 2021 12:30:31: 17000000 INFO @ Fri, 10 Dec 2021 12:30:32: 12000000 INFO @ Fri, 10 Dec 2021 12:30:37: 18000000 INFO @ Fri, 10 Dec 2021 12:30:38: 13000000 INFO @ Fri, 10 Dec 2021 12:30:38: 21000000 INFO @ Fri, 10 Dec 2021 12:30:43: 19000000 INFO @ Fri, 10 Dec 2021 12:30:44: 14000000 INFO @ Fri, 10 Dec 2021 12:30:45: 22000000 INFO @ Fri, 10 Dec 2021 12:30:49: 20000000 INFO @ Fri, 10 Dec 2021 12:30:49: 15000000 INFO @ Fri, 10 Dec 2021 12:30:51: 23000000 INFO @ Fri, 10 Dec 2021 12:30:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:30:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:30:54: #1 total tags in treatment: 23379853 INFO @ Fri, 10 Dec 2021 12:30:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:30:54: #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 12:30:55: #1 tags after filtering in treatment: 23379853 INFO @ Fri, 10 Dec 2021 12:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:30:55: #1 finished! INFO @ Fri, 10 Dec 2021 12:30:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:30:55: 21000000 INFO @ Fri, 10 Dec 2021 12:30:55: 16000000 INFO @ Fri, 10 Dec 2021 12:30:56: #2 number of paired peaks: 560 WARNING @ Fri, 10 Dec 2021 12:30:56: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Fri, 10 Dec 2021 12:30:56: start model_add_line... INFO @ Fri, 10 Dec 2021 12:30:56: start X-correlation... INFO @ Fri, 10 Dec 2021 12:30:56: end of X-cor INFO @ Fri, 10 Dec 2021 12:30:56: #2 finished! INFO @ Fri, 10 Dec 2021 12:30:56: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:30:56: #2 alternative fragment length(s) may be 2,33,577 bps INFO @ Fri, 10 Dec 2021 12:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.05_model.r WARNING @ Fri, 10 Dec 2021 12:30:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:30:56: #2 You may need to consider one of the other alternative d(s): 2,33,577 WARNING @ Fri, 10 Dec 2021 12:30:56: #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 12:30:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:30:56: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:31:01: 22000000 INFO @ Fri, 10 Dec 2021 12:31:01: 17000000 INFO @ Fri, 10 Dec 2021 12:31:06: 18000000 INFO @ Fri, 10 Dec 2021 12:31:06: 23000000 INFO @ Fri, 10 Dec 2021 12:31:09: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:31:09: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:31:09: #1 total tags in treatment: 23379853 INFO @ Fri, 10 Dec 2021 12:31:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:31:09: #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 12:31:09: #1 tags after filtering in treatment: 23379853 INFO @ Fri, 10 Dec 2021 12:31:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:31:09: #1 finished! INFO @ Fri, 10 Dec 2021 12:31:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:31:11: #2 number of paired peaks: 560 WARNING @ Fri, 10 Dec 2021 12:31:11: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Fri, 10 Dec 2021 12:31:11: start model_add_line... INFO @ Fri, 10 Dec 2021 12:31:11: start X-correlation... INFO @ Fri, 10 Dec 2021 12:31:11: end of X-cor INFO @ Fri, 10 Dec 2021 12:31:11: #2 finished! INFO @ Fri, 10 Dec 2021 12:31:11: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:31:11: #2 alternative fragment length(s) may be 2,33,577 bps INFO @ Fri, 10 Dec 2021 12:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.10_model.r WARNING @ Fri, 10 Dec 2021 12:31:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:31:11: #2 You may need to consider one of the other alternative d(s): 2,33,577 WARNING @ Fri, 10 Dec 2021 12:31:11: #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 12:31:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:31:12: 19000000 INFO @ Fri, 10 Dec 2021 12:31:17: 20000000 INFO @ Fri, 10 Dec 2021 12:31:22: 21000000 INFO @ Fri, 10 Dec 2021 12:31:27: 22000000 INFO @ Fri, 10 Dec 2021 12:31:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:31:32: 23000000 INFO @ Fri, 10 Dec 2021 12:31:34: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:31:34: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:31:34: #1 total tags in treatment: 23379853 INFO @ Fri, 10 Dec 2021 12:31:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:31:34: #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 12:31:35: #1 tags after filtering in treatment: 23379853 INFO @ Fri, 10 Dec 2021 12:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:31:35: #1 finished! INFO @ Fri, 10 Dec 2021 12:31:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:31:37: #2 number of paired peaks: 560 WARNING @ Fri, 10 Dec 2021 12:31:37: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Fri, 10 Dec 2021 12:31:37: start model_add_line... INFO @ Fri, 10 Dec 2021 12:31:37: start X-correlation... INFO @ Fri, 10 Dec 2021 12:31:37: end of X-cor INFO @ Fri, 10 Dec 2021 12:31:37: #2 finished! INFO @ Fri, 10 Dec 2021 12:31:37: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:31:37: #2 alternative fragment length(s) may be 2,33,577 bps INFO @ Fri, 10 Dec 2021 12:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.20_model.r WARNING @ Fri, 10 Dec 2021 12:31:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:31:37: #2 You may need to consider one of the other alternative d(s): 2,33,577 WARNING @ Fri, 10 Dec 2021 12:31:37: #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 12:31:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:31:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.05_summits.bed INFO @ Fri, 10 Dec 2021 12:31:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.10_summits.bed INFO @ Fri, 10 Dec 2021 12:32:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:32:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574269/SRX8574269.20_summits.bed INFO @ Fri, 10 Dec 2021 12:32:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling