Job ID = 14167399 SRX = SRX8574260 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: 00:09:31 39301965 reads; of these: 39301965 (100.00%) were unpaired; of these: 2828589 (7.20%) aligned 0 times 27793008 (70.72%) aligned exactly 1 time 8680368 (22.09%) aligned >1 times 92.80% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 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 16 files... [bam_rmdupse_core] 12470468 / 36473376 = 0.3419 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 12:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.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 12:24:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:24:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:24:41: 1000000 INFO @ Fri, 10 Dec 2021 12:24:45: 2000000 INFO @ Fri, 10 Dec 2021 12:24:50: 3000000 INFO @ Fri, 10 Dec 2021 12:24:54: 4000000 INFO @ Fri, 10 Dec 2021 12:24:59: 5000000 INFO @ Fri, 10 Dec 2021 12:25:03: 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 12:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.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 12:25:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:25:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:25:08: 7000000 INFO @ Fri, 10 Dec 2021 12:25:11: 1000000 INFO @ Fri, 10 Dec 2021 12:25:13: 8000000 INFO @ Fri, 10 Dec 2021 12:25:17: 2000000 INFO @ Fri, 10 Dec 2021 12:25:17: 9000000 INFO @ Fri, 10 Dec 2021 12:25:22: 3000000 INFO @ Fri, 10 Dec 2021 12:25:22: 10000000 INFO @ Fri, 10 Dec 2021 12:25:27: 11000000 INFO @ Fri, 10 Dec 2021 12:25:27: 4000000 INFO @ Fri, 10 Dec 2021 12:25:32: 12000000 INFO @ Fri, 10 Dec 2021 12:25:33: 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 @ Fri, 10 Dec 2021 12:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.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 12:25:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:25:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:25:37: 13000000 INFO @ Fri, 10 Dec 2021 12:25:38: 6000000 INFO @ Fri, 10 Dec 2021 12:25:42: 14000000 INFO @ Fri, 10 Dec 2021 12:25:42: 1000000 INFO @ Fri, 10 Dec 2021 12:25:44: 7000000 INFO @ Fri, 10 Dec 2021 12:25:46: 15000000 INFO @ Fri, 10 Dec 2021 12:25:47: 2000000 INFO @ Fri, 10 Dec 2021 12:25:49: 8000000 INFO @ Fri, 10 Dec 2021 12:25:51: 16000000 INFO @ Fri, 10 Dec 2021 12:25:53: 3000000 INFO @ Fri, 10 Dec 2021 12:25:54: 9000000 INFO @ Fri, 10 Dec 2021 12:25:56: 17000000 INFO @ Fri, 10 Dec 2021 12:25:58: 4000000 INFO @ Fri, 10 Dec 2021 12:26:00: 10000000 INFO @ Fri, 10 Dec 2021 12:26:01: 18000000 INFO @ Fri, 10 Dec 2021 12:26:04: 5000000 INFO @ Fri, 10 Dec 2021 12:26:05: 11000000 INFO @ Fri, 10 Dec 2021 12:26:06: 19000000 INFO @ Fri, 10 Dec 2021 12:26:09: 6000000 INFO @ Fri, 10 Dec 2021 12:26:11: 12000000 INFO @ Fri, 10 Dec 2021 12:26:11: 20000000 INFO @ Fri, 10 Dec 2021 12:26:15: 7000000 INFO @ Fri, 10 Dec 2021 12:26:16: 21000000 INFO @ Fri, 10 Dec 2021 12:26:16: 13000000 INFO @ Fri, 10 Dec 2021 12:26:21: 8000000 INFO @ Fri, 10 Dec 2021 12:26:21: 22000000 INFO @ Fri, 10 Dec 2021 12:26:22: 14000000 INFO @ Fri, 10 Dec 2021 12:26:26: 23000000 INFO @ Fri, 10 Dec 2021 12:26:26: 9000000 INFO @ Fri, 10 Dec 2021 12:26:27: 15000000 INFO @ Fri, 10 Dec 2021 12:26:31: 24000000 INFO @ Fri, 10 Dec 2021 12:26:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:26:31: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:26:31: #1 total tags in treatment: 24002908 INFO @ Fri, 10 Dec 2021 12:26:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:26:31: #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 12:26:32: #1 tags after filtering in treatment: 24002908 INFO @ Fri, 10 Dec 2021 12:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:26:32: #1 finished! INFO @ Fri, 10 Dec 2021 12:26:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:26:32: 10000000 INFO @ Fri, 10 Dec 2021 12:26:32: 16000000 INFO @ Fri, 10 Dec 2021 12:26:33: #2 number of paired peaks: 345 WARNING @ Fri, 10 Dec 2021 12:26:33: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 10 Dec 2021 12:26:33: start model_add_line... INFO @ Fri, 10 Dec 2021 12:26:33: start X-correlation... INFO @ Fri, 10 Dec 2021 12:26:33: end of X-cor INFO @ Fri, 10 Dec 2021 12:26:33: #2 finished! INFO @ Fri, 10 Dec 2021 12:26:33: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:26:33: #2 alternative fragment length(s) may be 2,41,568 bps INFO @ Fri, 10 Dec 2021 12:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.05_model.r WARNING @ Fri, 10 Dec 2021 12:26:33: #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 12:26:33: #2 You may need to consider one of the other alternative d(s): 2,41,568 WARNING @ Fri, 10 Dec 2021 12:26:33: #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 12:26:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:26:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:26:38: 11000000 INFO @ Fri, 10 Dec 2021 12:26:38: 17000000 INFO @ Fri, 10 Dec 2021 12:26:43: 12000000 INFO @ Fri, 10 Dec 2021 12:26:43: 18000000 INFO @ Fri, 10 Dec 2021 12:26:49: 19000000 INFO @ Fri, 10 Dec 2021 12:26:49: 13000000 INFO @ Fri, 10 Dec 2021 12:26:54: 20000000 INFO @ Fri, 10 Dec 2021 12:26:55: 14000000 INFO @ Fri, 10 Dec 2021 12:27:00: 21000000 INFO @ Fri, 10 Dec 2021 12:27:00: 15000000 INFO @ Fri, 10 Dec 2021 12:27:05: 22000000 INFO @ Fri, 10 Dec 2021 12:27:06: 16000000 INFO @ Fri, 10 Dec 2021 12:27:11: 23000000 INFO @ Fri, 10 Dec 2021 12:27:12: 17000000 INFO @ Fri, 10 Dec 2021 12:27:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:27:16: 24000000 INFO @ Fri, 10 Dec 2021 12:27:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:27:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:27:17: #1 total tags in treatment: 24002908 INFO @ Fri, 10 Dec 2021 12:27:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:27:17: #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 12:27:17: 18000000 INFO @ Fri, 10 Dec 2021 12:27:17: #1 tags after filtering in treatment: 24002908 INFO @ Fri, 10 Dec 2021 12:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:27:17: #1 finished! INFO @ Fri, 10 Dec 2021 12:27:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:27:19: #2 number of paired peaks: 345 WARNING @ Fri, 10 Dec 2021 12:27:19: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 10 Dec 2021 12:27:19: start model_add_line... INFO @ Fri, 10 Dec 2021 12:27:19: start X-correlation... INFO @ Fri, 10 Dec 2021 12:27:19: end of X-cor INFO @ Fri, 10 Dec 2021 12:27:19: #2 finished! INFO @ Fri, 10 Dec 2021 12:27:19: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:27:19: #2 alternative fragment length(s) may be 2,41,568 bps INFO @ Fri, 10 Dec 2021 12:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.10_model.r WARNING @ Fri, 10 Dec 2021 12:27:19: #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 12:27:19: #2 You may need to consider one of the other alternative d(s): 2,41,568 WARNING @ Fri, 10 Dec 2021 12:27:19: #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 12:27:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:27:23: 19000000 INFO @ Fri, 10 Dec 2021 12:27:28: 20000000 INFO @ Fri, 10 Dec 2021 12:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.05_summits.bed INFO @ Fri, 10 Dec 2021 12:27:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:27:34: 21000000 INFO @ Fri, 10 Dec 2021 12:27:39: 22000000 INFO @ Fri, 10 Dec 2021 12:27:45: 23000000 INFO @ Fri, 10 Dec 2021 12:27:51: 24000000 INFO @ Fri, 10 Dec 2021 12:27:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:27:51: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:27:51: #1 total tags in treatment: 24002908 INFO @ Fri, 10 Dec 2021 12:27:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:27:51: #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 12:27:51: #1 tags after filtering in treatment: 24002908 INFO @ Fri, 10 Dec 2021 12:27:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:27:51: #1 finished! INFO @ Fri, 10 Dec 2021 12:27:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:27:53: #2 number of paired peaks: 345 WARNING @ Fri, 10 Dec 2021 12:27:53: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 10 Dec 2021 12:27:53: start model_add_line... INFO @ Fri, 10 Dec 2021 12:27:53: start X-correlation... INFO @ Fri, 10 Dec 2021 12:27:53: end of X-cor INFO @ Fri, 10 Dec 2021 12:27:53: #2 finished! INFO @ Fri, 10 Dec 2021 12:27:53: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:27:53: #2 alternative fragment length(s) may be 2,41,568 bps INFO @ Fri, 10 Dec 2021 12:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.20_model.r WARNING @ Fri, 10 Dec 2021 12:27:53: #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 12:27:53: #2 You may need to consider one of the other alternative d(s): 2,41,568 WARNING @ Fri, 10 Dec 2021 12:27:53: #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 12:27:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:27:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.10_summits.bed INFO @ Fri, 10 Dec 2021 12:28:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:28:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574260/SRX8574260.20_summits.bed INFO @ Fri, 10 Dec 2021 12:28:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling