Job ID = 14171072 SRX = SRX9434463 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: 00:13:14 39741127 reads; of these: 39741127 (100.00%) were unpaired; of these: 1093028 (2.75%) aligned 0 times 26686513 (67.15%) aligned exactly 1 time 11961586 (30.10%) aligned >1 times 97.25% overall alignment rate Time searching: 00:13:14 Overall time: 00:13:14 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] 10809174 / 38648099 = 0.2797 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 09:43:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.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 09:43:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:23: 1000000 INFO @ Sat, 11 Dec 2021 09:43:30: 2000000 INFO @ Sat, 11 Dec 2021 09:43:38: 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 09:43:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.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 09:43:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:45: 4000000 INFO @ Sat, 11 Dec 2021 09:43:53: 5000000 INFO @ Sat, 11 Dec 2021 09:43:55: 1000000 INFO @ Sat, 11 Dec 2021 09:44:01: 6000000 INFO @ Sat, 11 Dec 2021 09:44:06: 2000000 INFO @ Sat, 11 Dec 2021 09:44:08: 7000000 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 09:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.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 09:44:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:44:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:44:16: 3000000 INFO @ Sat, 11 Dec 2021 09:44:16: 8000000 INFO @ Sat, 11 Dec 2021 09:44:23: 1000000 INFO @ Sat, 11 Dec 2021 09:44:23: 9000000 INFO @ Sat, 11 Dec 2021 09:44:25: 4000000 INFO @ Sat, 11 Dec 2021 09:44:31: 10000000 INFO @ Sat, 11 Dec 2021 09:44:31: 2000000 INFO @ Sat, 11 Dec 2021 09:44:35: 5000000 INFO @ Sat, 11 Dec 2021 09:44:40: 11000000 INFO @ Sat, 11 Dec 2021 09:44:40: 3000000 INFO @ Sat, 11 Dec 2021 09:44:44: 6000000 INFO @ Sat, 11 Dec 2021 09:44:48: 12000000 INFO @ Sat, 11 Dec 2021 09:44:49: 4000000 INFO @ Sat, 11 Dec 2021 09:44:54: 7000000 INFO @ Sat, 11 Dec 2021 09:44:57: 13000000 INFO @ Sat, 11 Dec 2021 09:44:58: 5000000 INFO @ Sat, 11 Dec 2021 09:45:04: 8000000 INFO @ Sat, 11 Dec 2021 09:45:06: 14000000 INFO @ Sat, 11 Dec 2021 09:45:07: 6000000 INFO @ Sat, 11 Dec 2021 09:45:13: 9000000 INFO @ Sat, 11 Dec 2021 09:45:14: 15000000 INFO @ Sat, 11 Dec 2021 09:45:15: 7000000 INFO @ Sat, 11 Dec 2021 09:45:22: 10000000 INFO @ Sat, 11 Dec 2021 09:45:22: 16000000 INFO @ Sat, 11 Dec 2021 09:45:24: 8000000 INFO @ Sat, 11 Dec 2021 09:45:31: 17000000 INFO @ Sat, 11 Dec 2021 09:45:31: 11000000 INFO @ Sat, 11 Dec 2021 09:45:32: 9000000 INFO @ Sat, 11 Dec 2021 09:45:39: 18000000 INFO @ Sat, 11 Dec 2021 09:45:40: 10000000 INFO @ Sat, 11 Dec 2021 09:45:41: 12000000 INFO @ Sat, 11 Dec 2021 09:45:47: 19000000 INFO @ Sat, 11 Dec 2021 09:45:49: 11000000 INFO @ Sat, 11 Dec 2021 09:45:50: 13000000 INFO @ Sat, 11 Dec 2021 09:45:55: 20000000 INFO @ Sat, 11 Dec 2021 09:45:58: 12000000 INFO @ Sat, 11 Dec 2021 09:46:00: 14000000 INFO @ Sat, 11 Dec 2021 09:46:05: 21000000 INFO @ Sat, 11 Dec 2021 09:46:06: 13000000 INFO @ Sat, 11 Dec 2021 09:46:09: 15000000 INFO @ Sat, 11 Dec 2021 09:46:13: 22000000 INFO @ Sat, 11 Dec 2021 09:46:13: 14000000 INFO @ Sat, 11 Dec 2021 09:46:18: 16000000 INFO @ Sat, 11 Dec 2021 09:46:21: 15000000 INFO @ Sat, 11 Dec 2021 09:46:21: 23000000 INFO @ Sat, 11 Dec 2021 09:46:27: 17000000 INFO @ Sat, 11 Dec 2021 09:46:29: 16000000 INFO @ Sat, 11 Dec 2021 09:46:29: 24000000 INFO @ Sat, 11 Dec 2021 09:46:36: 17000000 INFO @ Sat, 11 Dec 2021 09:46:36: 25000000 INFO @ Sat, 11 Dec 2021 09:46:36: 18000000 INFO @ Sat, 11 Dec 2021 09:46:44: 18000000 INFO @ Sat, 11 Dec 2021 09:46:44: 26000000 INFO @ Sat, 11 Dec 2021 09:46:45: 19000000 INFO @ Sat, 11 Dec 2021 09:46:51: 19000000 INFO @ Sat, 11 Dec 2021 09:46:51: 27000000 INFO @ Sat, 11 Dec 2021 09:46:54: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:46:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:46:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:46:58: #1 total tags in treatment: 27838925 INFO @ Sat, 11 Dec 2021 09:46:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:58: #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 09:46:59: 20000000 INFO @ Sat, 11 Dec 2021 09:46:59: #1 tags after filtering in treatment: 27838881 INFO @ Sat, 11 Dec 2021 09:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:46:59: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:47:01: #2 number of paired peaks: 768 WARNING @ Sat, 11 Dec 2021 09:47:01: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 11 Dec 2021 09:47:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:47:02: start X-correlation... INFO @ Sat, 11 Dec 2021 09:47:02: end of X-cor INFO @ Sat, 11 Dec 2021 09:47:02: #2 finished! INFO @ Sat, 11 Dec 2021 09:47:02: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:47:02: #2 alternative fragment length(s) may be 1,17 bps INFO @ Sat, 11 Dec 2021 09:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.05_model.r WARNING @ Sat, 11 Dec 2021 09:47:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:47:02: #2 You may need to consider one of the other alternative d(s): 1,17 WARNING @ Sat, 11 Dec 2021 09:47:02: #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 09:47:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:47:04: 21000000 INFO @ Sat, 11 Dec 2021 09:47:06: 21000000 INFO @ Sat, 11 Dec 2021 09:47:14: 22000000 INFO @ Sat, 11 Dec 2021 09:47:14: 22000000 INFO @ Sat, 11 Dec 2021 09:47:22: 23000000 INFO @ Sat, 11 Dec 2021 09:47:23: 23000000 INFO @ Sat, 11 Dec 2021 09:47:30: 24000000 INFO @ Sat, 11 Dec 2021 09:47:32: 24000000 INFO @ Sat, 11 Dec 2021 09:47:37: 25000000 INFO @ Sat, 11 Dec 2021 09:47:41: 25000000 INFO @ Sat, 11 Dec 2021 09:47:44: 26000000 INFO @ Sat, 11 Dec 2021 09:47:50: 26000000 INFO @ Sat, 11 Dec 2021 09:47:52: 27000000 INFO @ Sat, 11 Dec 2021 09:47:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:47:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:47:58: #1 total tags in treatment: 27838925 INFO @ Sat, 11 Dec 2021 09:47:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:47:58: #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 09:47:59: #1 tags after filtering in treatment: 27838881 INFO @ Sat, 11 Dec 2021 09:47:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:47:59: #1 finished! INFO @ Sat, 11 Dec 2021 09:47:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:47:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:47:59: 27000000 INFO @ Sat, 11 Dec 2021 09:48:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:48:01: #2 number of paired peaks: 768 WARNING @ Sat, 11 Dec 2021 09:48:01: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 11 Dec 2021 09:48:01: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:02: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:02: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:02: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:02: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:48:02: #2 alternative fragment length(s) may be 1,17 bps INFO @ Sat, 11 Dec 2021 09:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.20_model.r WARNING @ Sat, 11 Dec 2021 09:48:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:48:02: #2 You may need to consider one of the other alternative d(s): 1,17 WARNING @ Sat, 11 Dec 2021 09:48:02: #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 09:48:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:48:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:48:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:48:07: #1 total tags in treatment: 27838925 INFO @ Sat, 11 Dec 2021 09:48:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:48:07: #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 09:48:08: #1 tags after filtering in treatment: 27838881 INFO @ Sat, 11 Dec 2021 09:48:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:48:08: #1 finished! INFO @ Sat, 11 Dec 2021 09:48:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:48:10: #2 number of paired peaks: 768 WARNING @ Sat, 11 Dec 2021 09:48:10: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 11 Dec 2021 09:48:10: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:10: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:10: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:10: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:10: #2 predicted fragment length is 1 bps INFO @ Sat, 11 Dec 2021 09:48:10: #2 alternative fragment length(s) may be 1,17 bps INFO @ Sat, 11 Dec 2021 09:48:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.10_model.r WARNING @ Sat, 11 Dec 2021 09:48:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:48:10: #2 You may need to consider one of the other alternative d(s): 1,17 WARNING @ Sat, 11 Dec 2021 09:48:10: #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 09:48:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.05_summits.bed INFO @ Sat, 11 Dec 2021 09:48:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:49:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.20_summits.bed INFO @ Sat, 11 Dec 2021 09:49:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9434463/SRX9434463.10_summits.bed INFO @ Sat, 11 Dec 2021 09:49:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling