Job ID = 14167389 SRX = SRX8574258 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: 00:10:31 42824760 reads; of these: 42824760 (100.00%) were unpaired; of these: 3524351 (8.23%) aligned 0 times 29542461 (68.98%) aligned exactly 1 time 9757948 (22.79%) aligned >1 times 91.77% overall alignment rate Time searching: 00:10:31 Overall time: 00:10:31 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 20 files... [bam_rmdupse_core] 10630441 / 39300409 = 0.2705 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 12:23:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.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 12:23:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:23:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:23:21: 1000000 INFO @ Fri, 10 Dec 2021 12:23:26: 2000000 INFO @ Fri, 10 Dec 2021 12:23:30: 3000000 INFO @ Fri, 10 Dec 2021 12:23:35: 4000000 INFO @ Fri, 10 Dec 2021 12:23:40: 5000000 INFO @ Fri, 10 Dec 2021 12:23:44: 6000000 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 12:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.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 12:23:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:23:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:23:49: 7000000 INFO @ Fri, 10 Dec 2021 12:23:52: 1000000 INFO @ Fri, 10 Dec 2021 12:23:54: 8000000 INFO @ Fri, 10 Dec 2021 12:23:58: 2000000 INFO @ Fri, 10 Dec 2021 12:24:00: 9000000 INFO @ Fri, 10 Dec 2021 12:24:04: 3000000 INFO @ Fri, 10 Dec 2021 12:24:05: 10000000 INFO @ Fri, 10 Dec 2021 12:24:10: 11000000 INFO @ Fri, 10 Dec 2021 12:24:10: 4000000 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 12:24:15: 12000000 INFO @ Fri, 10 Dec 2021 12:24:16: 5000000 INFO @ Fri, 10 Dec 2021 12:24:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.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 12:24:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:24:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:24:20: 13000000 INFO @ Fri, 10 Dec 2021 12:24:22: 1000000 INFO @ Fri, 10 Dec 2021 12:24:22: 6000000 INFO @ Fri, 10 Dec 2021 12:24:25: 14000000 INFO @ Fri, 10 Dec 2021 12:24:27: 2000000 INFO @ Fri, 10 Dec 2021 12:24:28: 7000000 INFO @ Fri, 10 Dec 2021 12:24:30: 15000000 INFO @ Fri, 10 Dec 2021 12:24:32: 3000000 INFO @ Fri, 10 Dec 2021 12:24:34: 8000000 INFO @ Fri, 10 Dec 2021 12:24:36: 16000000 INFO @ Fri, 10 Dec 2021 12:24:37: 4000000 INFO @ Fri, 10 Dec 2021 12:24:40: 9000000 INFO @ Fri, 10 Dec 2021 12:24:41: 17000000 INFO @ Fri, 10 Dec 2021 12:24:43: 5000000 INFO @ Fri, 10 Dec 2021 12:24:46: 10000000 INFO @ Fri, 10 Dec 2021 12:24:46: 18000000 INFO @ Fri, 10 Dec 2021 12:24:49: 6000000 INFO @ Fri, 10 Dec 2021 12:24:52: 19000000 INFO @ Fri, 10 Dec 2021 12:24:52: 11000000 INFO @ Fri, 10 Dec 2021 12:24:54: 7000000 INFO @ Fri, 10 Dec 2021 12:24:57: 20000000 INFO @ Fri, 10 Dec 2021 12:24:58: 12000000 INFO @ Fri, 10 Dec 2021 12:24:59: 8000000 INFO @ Fri, 10 Dec 2021 12:25:02: 21000000 INFO @ Fri, 10 Dec 2021 12:25:03: 13000000 INFO @ Fri, 10 Dec 2021 12:25:04: 9000000 INFO @ Fri, 10 Dec 2021 12:25:07: 22000000 INFO @ Fri, 10 Dec 2021 12:25:09: 10000000 INFO @ Fri, 10 Dec 2021 12:25:09: 14000000 INFO @ Fri, 10 Dec 2021 12:25:12: 23000000 INFO @ Fri, 10 Dec 2021 12:25:14: 11000000 INFO @ Fri, 10 Dec 2021 12:25:15: 15000000 INFO @ Fri, 10 Dec 2021 12:25:17: 24000000 INFO @ Fri, 10 Dec 2021 12:25:19: 12000000 INFO @ Fri, 10 Dec 2021 12:25:21: 16000000 INFO @ Fri, 10 Dec 2021 12:25:22: 25000000 INFO @ Fri, 10 Dec 2021 12:25:24: 13000000 INFO @ Fri, 10 Dec 2021 12:25:27: 17000000 INFO @ Fri, 10 Dec 2021 12:25:28: 26000000 INFO @ Fri, 10 Dec 2021 12:25:29: 14000000 INFO @ Fri, 10 Dec 2021 12:25:33: 27000000 INFO @ Fri, 10 Dec 2021 12:25:33: 18000000 INFO @ Fri, 10 Dec 2021 12:25:34: 15000000 INFO @ Fri, 10 Dec 2021 12:25:38: 28000000 INFO @ Fri, 10 Dec 2021 12:25:39: 19000000 INFO @ Fri, 10 Dec 2021 12:25:40: 16000000 INFO @ Fri, 10 Dec 2021 12:25:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:25:42: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:25:42: #1 total tags in treatment: 28669968 INFO @ Fri, 10 Dec 2021 12:25:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:25:42: #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 12:25:42: #1 tags after filtering in treatment: 28669968 INFO @ Fri, 10 Dec 2021 12:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:25:42: #1 finished! INFO @ Fri, 10 Dec 2021 12:25:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:25:44: #2 number of paired peaks: 202 WARNING @ Fri, 10 Dec 2021 12:25:44: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 10 Dec 2021 12:25:44: start model_add_line... INFO @ Fri, 10 Dec 2021 12:25:44: start X-correlation... INFO @ Fri, 10 Dec 2021 12:25:44: end of X-cor INFO @ Fri, 10 Dec 2021 12:25:44: #2 finished! INFO @ Fri, 10 Dec 2021 12:25:44: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:25:44: #2 alternative fragment length(s) may be 1,20,37 bps INFO @ Fri, 10 Dec 2021 12:25:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.05_model.r WARNING @ Fri, 10 Dec 2021 12:25:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:25:44: #2 You may need to consider one of the other alternative d(s): 1,20,37 WARNING @ Fri, 10 Dec 2021 12:25:44: #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 12:25:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:25:45: 17000000 INFO @ Fri, 10 Dec 2021 12:25:45: 20000000 INFO @ Fri, 10 Dec 2021 12:25:50: 18000000 INFO @ Fri, 10 Dec 2021 12:25:51: 21000000 INFO @ Fri, 10 Dec 2021 12:25:55: 19000000 INFO @ Fri, 10 Dec 2021 12:25:56: 22000000 INFO @ Fri, 10 Dec 2021 12:26:00: 20000000 INFO @ Fri, 10 Dec 2021 12:26:02: 23000000 INFO @ Fri, 10 Dec 2021 12:26:05: 21000000 INFO @ Fri, 10 Dec 2021 12:26:08: 24000000 INFO @ Fri, 10 Dec 2021 12:26:10: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:26:14: 25000000 INFO @ Fri, 10 Dec 2021 12:26:16: 23000000 INFO @ Fri, 10 Dec 2021 12:26:20: 26000000 INFO @ Fri, 10 Dec 2021 12:26:21: 24000000 INFO @ Fri, 10 Dec 2021 12:26:26: 25000000 INFO @ Fri, 10 Dec 2021 12:26:26: 27000000 INFO @ Fri, 10 Dec 2021 12:26:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:26:31: 26000000 INFO @ Fri, 10 Dec 2021 12:26:32: 28000000 INFO @ Fri, 10 Dec 2021 12:26:36: 27000000 INFO @ Fri, 10 Dec 2021 12:26:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:26:36: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:26:36: #1 total tags in treatment: 28669968 INFO @ Fri, 10 Dec 2021 12:26:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:26:36: #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 12:26:37: #1 tags after filtering in treatment: 28669968 INFO @ Fri, 10 Dec 2021 12:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:26:37: #1 finished! INFO @ Fri, 10 Dec 2021 12:26:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:26:39: #2 number of paired peaks: 202 WARNING @ Fri, 10 Dec 2021 12:26:39: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 10 Dec 2021 12:26:39: start model_add_line... INFO @ Fri, 10 Dec 2021 12:26:39: start X-correlation... INFO @ Fri, 10 Dec 2021 12:26:39: end of X-cor INFO @ Fri, 10 Dec 2021 12:26:39: #2 finished! INFO @ Fri, 10 Dec 2021 12:26:39: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:26:39: #2 alternative fragment length(s) may be 1,20,37 bps INFO @ Fri, 10 Dec 2021 12:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.10_model.r WARNING @ Fri, 10 Dec 2021 12:26:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:26:39: #2 You may need to consider one of the other alternative d(s): 1,20,37 WARNING @ Fri, 10 Dec 2021 12:26:39: #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 12:26:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:26:41: 28000000 INFO @ Fri, 10 Dec 2021 12:26:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:26:45: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:26:45: #1 total tags in treatment: 28669968 INFO @ Fri, 10 Dec 2021 12:26:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:26:45: #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 12:26:45: #1 tags after filtering in treatment: 28669968 INFO @ Fri, 10 Dec 2021 12:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:26:45: #1 finished! INFO @ Fri, 10 Dec 2021 12:26:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:26:47: #2 number of paired peaks: 202 WARNING @ Fri, 10 Dec 2021 12:26:47: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Fri, 10 Dec 2021 12:26:47: start model_add_line... INFO @ Fri, 10 Dec 2021 12:26:47: start X-correlation... INFO @ Fri, 10 Dec 2021 12:26:47: end of X-cor INFO @ Fri, 10 Dec 2021 12:26:47: #2 finished! INFO @ Fri, 10 Dec 2021 12:26:47: #2 predicted fragment length is 1 bps INFO @ Fri, 10 Dec 2021 12:26:47: #2 alternative fragment length(s) may be 1,20,37 bps INFO @ Fri, 10 Dec 2021 12:26:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.20_model.r WARNING @ Fri, 10 Dec 2021 12:26:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:26:48: #2 You may need to consider one of the other alternative d(s): 1,20,37 WARNING @ Fri, 10 Dec 2021 12:26:48: #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 12:26:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:26:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:26:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.05_summits.bed INFO @ Fri, 10 Dec 2021 12:26:49: 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 12:27:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:27:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.10_summits.bed INFO @ Fri, 10 Dec 2021 12:27:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574258/SRX8574258.20_summits.bed INFO @ Fri, 10 Dec 2021 12:27:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling