Job ID = 14168051 SRX = SRX8688943 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:50 21669635 reads; of these: 21669635 (100.00%) were unpaired; of these: 6906974 (31.87%) aligned 0 times 11486892 (53.01%) aligned exactly 1 time 3275769 (15.12%) aligned >1 times 68.13% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 8 files... [bam_rmdupse_core] 1326150 / 14762661 = 0.0898 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 14:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.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 14:55:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:55:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:56:01: 1000000 INFO @ Fri, 10 Dec 2021 14:56:10: 2000000 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 14:56:18: 3000000 INFO @ Fri, 10 Dec 2021 14:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.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 14:56:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:56:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:56:27: 4000000 INFO @ Fri, 10 Dec 2021 14:56:29: 1000000 INFO @ Fri, 10 Dec 2021 14:56:35: 5000000 INFO @ Fri, 10 Dec 2021 14:56:37: 2000000 INFO @ Fri, 10 Dec 2021 14:56:44: 6000000 INFO @ Fri, 10 Dec 2021 14:56:45: 3000000 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 14:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.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 14:56:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:56:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:56:52: 7000000 INFO @ Fri, 10 Dec 2021 14:56:54: 4000000 INFO @ Fri, 10 Dec 2021 14:57:00: 1000000 INFO @ Fri, 10 Dec 2021 14:57:01: 8000000 INFO @ Fri, 10 Dec 2021 14:57:02: 5000000 INFO @ Fri, 10 Dec 2021 14:57:09: 2000000 INFO @ Fri, 10 Dec 2021 14:57:10: 9000000 INFO @ Fri, 10 Dec 2021 14:57:11: 6000000 INFO @ Fri, 10 Dec 2021 14:57:19: 3000000 INFO @ Fri, 10 Dec 2021 14:57:19: 10000000 INFO @ Fri, 10 Dec 2021 14:57:19: 7000000 INFO @ Fri, 10 Dec 2021 14:57:28: 4000000 INFO @ Fri, 10 Dec 2021 14:57:28: 8000000 INFO @ Fri, 10 Dec 2021 14:57:29: 11000000 INFO @ Fri, 10 Dec 2021 14:57:36: 9000000 INFO @ Fri, 10 Dec 2021 14:57:37: 5000000 INFO @ Fri, 10 Dec 2021 14:57:37: 12000000 INFO @ Fri, 10 Dec 2021 14:57:45: 10000000 INFO @ Fri, 10 Dec 2021 14:57:45: 6000000 INFO @ Fri, 10 Dec 2021 14:57:46: 13000000 INFO @ Fri, 10 Dec 2021 14:57:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:57:50: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:57:50: #1 total tags in treatment: 13436511 INFO @ Fri, 10 Dec 2021 14:57:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:57:50: #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 14:57:51: #1 tags after filtering in treatment: 13436428 INFO @ Fri, 10 Dec 2021 14:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:57:51: #1 finished! INFO @ Fri, 10 Dec 2021 14:57:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:57:52: #2 number of paired peaks: 368 WARNING @ Fri, 10 Dec 2021 14:57:52: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Fri, 10 Dec 2021 14:57:52: start model_add_line... INFO @ Fri, 10 Dec 2021 14:57:52: start X-correlation... INFO @ Fri, 10 Dec 2021 14:57:52: end of X-cor INFO @ Fri, 10 Dec 2021 14:57:52: #2 finished! INFO @ Fri, 10 Dec 2021 14:57:52: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 14:57:52: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 10 Dec 2021 14:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.05_model.r WARNING @ Fri, 10 Dec 2021 14:57:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:57:53: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 10 Dec 2021 14:57:53: #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 14:57:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:57:54: 11000000 INFO @ Fri, 10 Dec 2021 14:57:54: 7000000 INFO @ Fri, 10 Dec 2021 14:58:02: 12000000 INFO @ Fri, 10 Dec 2021 14:58:03: 8000000 INFO @ Fri, 10 Dec 2021 14:58:11: 13000000 INFO @ Fri, 10 Dec 2021 14:58:12: 9000000 INFO @ Fri, 10 Dec 2021 14:58:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:58:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:58:15: #1 total tags in treatment: 13436511 INFO @ Fri, 10 Dec 2021 14:58:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:58:15: #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 14:58:16: #1 tags after filtering in treatment: 13436428 INFO @ Fri, 10 Dec 2021 14:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:58:16: #1 finished! INFO @ Fri, 10 Dec 2021 14:58:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:58:17: #2 number of paired peaks: 368 WARNING @ Fri, 10 Dec 2021 14:58:17: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Fri, 10 Dec 2021 14:58:17: start model_add_line... INFO @ Fri, 10 Dec 2021 14:58:17: start X-correlation... INFO @ Fri, 10 Dec 2021 14:58:17: end of X-cor INFO @ Fri, 10 Dec 2021 14:58:17: #2 finished! INFO @ Fri, 10 Dec 2021 14:58:17: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 14:58:17: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 10 Dec 2021 14:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.10_model.r WARNING @ Fri, 10 Dec 2021 14:58:17: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:58:17: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 10 Dec 2021 14:58:17: #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 14:58:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:58:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:58:22: 10000000 INFO @ Fri, 10 Dec 2021 14:58:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:58:32: 11000000 INFO @ Fri, 10 Dec 2021 14:58:41: 12000000 INFO @ Fri, 10 Dec 2021 14:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.05_summits.bed INFO @ Fri, 10 Dec 2021 14:58:49: Done! pass1 - making usageList (567 chroms): 2 millis pass2 - checking and writing primary data (2213 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:58:51: 13000000 INFO @ Fri, 10 Dec 2021 14:58:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:58:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:58:55: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:58:55: #1 total tags in treatment: 13436511 INFO @ Fri, 10 Dec 2021 14:58:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:58:55: #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 14:58:56: #1 tags after filtering in treatment: 13436428 INFO @ Fri, 10 Dec 2021 14:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:58:56: #1 finished! INFO @ Fri, 10 Dec 2021 14:58:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:58:57: #2 number of paired peaks: 368 WARNING @ Fri, 10 Dec 2021 14:58:57: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Fri, 10 Dec 2021 14:58:57: start model_add_line... INFO @ Fri, 10 Dec 2021 14:58:57: start X-correlation... INFO @ Fri, 10 Dec 2021 14:58:57: end of X-cor INFO @ Fri, 10 Dec 2021 14:58:57: #2 finished! INFO @ Fri, 10 Dec 2021 14:58:57: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 14:58:57: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 10 Dec 2021 14:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.20_model.r WARNING @ Fri, 10 Dec 2021 14:58:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:58:57: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 10 Dec 2021 14:58:57: #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 14:58:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:58:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:59:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:59:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:59:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.10_summits.bed INFO @ Fri, 10 Dec 2021 14:59:13: Done! pass1 - making usageList (346 chroms): 2 millis pass2 - checking and writing primary data (957 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:59:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:59:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688943/SRX8688943.20_summits.bed INFO @ Fri, 10 Dec 2021 14:59:54: Done! pass1 - making usageList (160 chroms): 2 millis pass2 - checking and writing primary data (302 records, 4 fields): 11 millis CompletedMACS2peakCalling