Job ID = 14171079 SRX = SRX9434466 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: 00:09:44 33625544 reads; of these: 33625544 (100.00%) were unpaired; of these: 925092 (2.75%) aligned 0 times 22784057 (67.76%) aligned exactly 1 time 9916395 (29.49%) aligned >1 times 97.25% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 8319458 / 32700452 = 0.2544 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 09:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.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 09:42:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:02: 1000000 INFO @ Sat, 11 Dec 2021 09:43:08: 2000000 INFO @ Sat, 11 Dec 2021 09:43:13: 3000000 INFO @ Sat, 11 Dec 2021 09:43:19: 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 @ Sat, 11 Dec 2021 09:43:25: 5000000 INFO @ Sat, 11 Dec 2021 09:43:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.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 09:43:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:31: 6000000 INFO @ Sat, 11 Dec 2021 09:43:33: 1000000 INFO @ Sat, 11 Dec 2021 09:43:37: 7000000 INFO @ Sat, 11 Dec 2021 09:43:40: 2000000 INFO @ Sat, 11 Dec 2021 09:43:43: 8000000 INFO @ Sat, 11 Dec 2021 09:43:47: 3000000 INFO @ Sat, 11 Dec 2021 09:43:49: 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 @ Sat, 11 Dec 2021 09:43:54: 4000000 INFO @ Sat, 11 Dec 2021 09:43:55: 10000000 INFO @ Sat, 11 Dec 2021 09:43:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.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 09:43:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:44:01: 5000000 INFO @ Sat, 11 Dec 2021 09:44:01: 11000000 INFO @ Sat, 11 Dec 2021 09:44:03: 1000000 INFO @ Sat, 11 Dec 2021 09:44:07: 12000000 INFO @ Sat, 11 Dec 2021 09:44:08: 6000000 INFO @ Sat, 11 Dec 2021 09:44:10: 2000000 INFO @ Sat, 11 Dec 2021 09:44:13: 13000000 INFO @ Sat, 11 Dec 2021 09:44:15: 7000000 INFO @ Sat, 11 Dec 2021 09:44:17: 3000000 INFO @ Sat, 11 Dec 2021 09:44:20: 14000000 INFO @ Sat, 11 Dec 2021 09:44:22: 8000000 INFO @ Sat, 11 Dec 2021 09:44:24: 4000000 INFO @ Sat, 11 Dec 2021 09:44:26: 15000000 INFO @ Sat, 11 Dec 2021 09:44:28: 9000000 INFO @ Sat, 11 Dec 2021 09:44:31: 5000000 INFO @ Sat, 11 Dec 2021 09:44:32: 16000000 INFO @ Sat, 11 Dec 2021 09:44:34: 10000000 INFO @ Sat, 11 Dec 2021 09:44:38: 6000000 INFO @ Sat, 11 Dec 2021 09:44:39: 17000000 INFO @ Sat, 11 Dec 2021 09:44:41: 11000000 INFO @ Sat, 11 Dec 2021 09:44:44: 7000000 INFO @ Sat, 11 Dec 2021 09:44:45: 18000000 INFO @ Sat, 11 Dec 2021 09:44:47: 12000000 INFO @ Sat, 11 Dec 2021 09:44:51: 8000000 INFO @ Sat, 11 Dec 2021 09:44:52: 19000000 INFO @ Sat, 11 Dec 2021 09:44:53: 13000000 INFO @ Sat, 11 Dec 2021 09:44:58: 9000000 INFO @ Sat, 11 Dec 2021 09:44:58: 20000000 INFO @ Sat, 11 Dec 2021 09:45:00: 14000000 INFO @ Sat, 11 Dec 2021 09:45:05: 10000000 INFO @ Sat, 11 Dec 2021 09:45:05: 21000000 INFO @ Sat, 11 Dec 2021 09:45:06: 15000000 INFO @ Sat, 11 Dec 2021 09:45:11: 22000000 INFO @ Sat, 11 Dec 2021 09:45:11: 11000000 INFO @ Sat, 11 Dec 2021 09:45:13: 16000000 INFO @ Sat, 11 Dec 2021 09:45:17: 23000000 INFO @ Sat, 11 Dec 2021 09:45:18: 12000000 INFO @ Sat, 11 Dec 2021 09:45:19: 17000000 INFO @ Sat, 11 Dec 2021 09:45:24: 24000000 INFO @ Sat, 11 Dec 2021 09:45:25: 18000000 INFO @ Sat, 11 Dec 2021 09:45:25: 13000000 INFO @ Sat, 11 Dec 2021 09:45:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:45:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:45:27: #1 total tags in treatment: 24380994 INFO @ Sat, 11 Dec 2021 09:45:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:45:27: #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 09:45:28: #1 tags after filtering in treatment: 24380938 INFO @ Sat, 11 Dec 2021 09:45:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:45:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:45:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:45:29: #2 number of paired peaks: 834 WARNING @ Sat, 11 Dec 2021 09:45:29: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Sat, 11 Dec 2021 09:45:29: start model_add_line... INFO @ Sat, 11 Dec 2021 09:45:29: start X-correlation... INFO @ Sat, 11 Dec 2021 09:45:30: end of X-cor INFO @ Sat, 11 Dec 2021 09:45:30: #2 finished! INFO @ Sat, 11 Dec 2021 09:45:30: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 09:45:30: #2 alternative fragment length(s) may be 2 bps INFO @ Sat, 11 Dec 2021 09:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.05_model.r WARNING @ Sat, 11 Dec 2021 09:45:30: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:45:30: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sat, 11 Dec 2021 09:45:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:45:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:45:32: 14000000 INFO @ Sat, 11 Dec 2021 09:45:32: 19000000 INFO @ Sat, 11 Dec 2021 09:45:38: 20000000 INFO @ Sat, 11 Dec 2021 09:45:39: 15000000 INFO @ Sat, 11 Dec 2021 09:45:44: 21000000 INFO @ Sat, 11 Dec 2021 09:45:45: 16000000 INFO @ Sat, 11 Dec 2021 09:45:50: 22000000 INFO @ Sat, 11 Dec 2021 09:45:52: 17000000 INFO @ Sat, 11 Dec 2021 09:45:56: 23000000 INFO @ Sat, 11 Dec 2021 09:45:59: 18000000 INFO @ Sat, 11 Dec 2021 09:46:03: 24000000 INFO @ Sat, 11 Dec 2021 09:46:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:46:06: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:46:06: #1 total tags in treatment: 24380994 INFO @ Sat, 11 Dec 2021 09:46:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:06: #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 09:46:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:46:07: #1 tags after filtering in treatment: 24380938 INFO @ Sat, 11 Dec 2021 09:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:46:07: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:07: 19000000 INFO @ Sat, 11 Dec 2021 09:46:08: #2 number of paired peaks: 834 WARNING @ Sat, 11 Dec 2021 09:46:08: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Sat, 11 Dec 2021 09:46:08: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:08: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:08: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:08: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:08: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 09:46:08: #2 alternative fragment length(s) may be 2 bps INFO @ Sat, 11 Dec 2021 09:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.10_model.r WARNING @ Sat, 11 Dec 2021 09:46:08: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:46:08: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sat, 11 Dec 2021 09:46:08: #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 09:46:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:14: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:46:20: 21000000 INFO @ Sat, 11 Dec 2021 09:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.05_summits.bed INFO @ Sat, 11 Dec 2021 09:46:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:46:27: 22000000 INFO @ Sat, 11 Dec 2021 09:46:34: 23000000 INFO @ Sat, 11 Dec 2021 09:46:41: 24000000 INFO @ Sat, 11 Dec 2021 09:46:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:46:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:46:44: #1 total tags in treatment: 24380994 INFO @ Sat, 11 Dec 2021 09:46:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:44: #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 09:46:45: #1 tags after filtering in treatment: 24380938 INFO @ Sat, 11 Dec 2021 09:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:46:45: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:46:47: #2 number of paired peaks: 834 WARNING @ Sat, 11 Dec 2021 09:46:47: Fewer paired peaks (834) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 834 pairs to build model! INFO @ Sat, 11 Dec 2021 09:46:47: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:47: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:47: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:47: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:47: #2 predicted fragment length is 2 bps INFO @ Sat, 11 Dec 2021 09:46:47: #2 alternative fragment length(s) may be 2 bps INFO @ Sat, 11 Dec 2021 09:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.20_model.r WARNING @ Sat, 11 Dec 2021 09:46:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:46:47: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sat, 11 Dec 2021 09:46:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:46:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.10_summits.bed INFO @ Sat, 11 Dec 2021 09:47:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:47:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9434466/SRX9434466.20_summits.bed INFO @ Sat, 11 Dec 2021 09:47:43: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling