Job ID = 14167559 SRX = SRX4712941 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: 00:06:59 26357554 reads; of these: 26357554 (100.00%) were unpaired; of these: 838011 (3.18%) aligned 0 times 18395990 (69.79%) aligned exactly 1 time 7123553 (27.03%) aligned >1 times 96.82% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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 12 files... [bam_rmdupse_core] 5447926 / 25519543 = 0.2135 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 12:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.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 12:49:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:49:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:49:07: 1000000 INFO @ Fri, 10 Dec 2021 12:49:12: 2000000 INFO @ Fri, 10 Dec 2021 12:49:16: 3000000 INFO @ Fri, 10 Dec 2021 12:49:21: 4000000 INFO @ Fri, 10 Dec 2021 12:49:26: 5000000 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 12:49:31: 6000000 INFO @ Fri, 10 Dec 2021 12:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.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 12:49:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:49:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:49:36: 7000000 INFO @ Fri, 10 Dec 2021 12:49:37: 1000000 INFO @ Fri, 10 Dec 2021 12:49:40: 8000000 INFO @ Fri, 10 Dec 2021 12:49:42: 2000000 INFO @ Fri, 10 Dec 2021 12:49:45: 9000000 INFO @ Fri, 10 Dec 2021 12:49:47: 3000000 INFO @ Fri, 10 Dec 2021 12:49:50: 10000000 INFO @ Fri, 10 Dec 2021 12:49:52: 4000000 INFO @ Fri, 10 Dec 2021 12:49:55: 11000000 INFO @ Fri, 10 Dec 2021 12:49:56: 5000000 BedGraph に変換中... INFO @ Fri, 10 Dec 2021 12:50:00: 12000000 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 12:50:01: 6000000 INFO @ Fri, 10 Dec 2021 12:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.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 12:50:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:50:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:50:05: 13000000 INFO @ Fri, 10 Dec 2021 12:50:06: 7000000 INFO @ Fri, 10 Dec 2021 12:50:07: 1000000 INFO @ Fri, 10 Dec 2021 12:50:10: 14000000 INFO @ Fri, 10 Dec 2021 12:50:11: 8000000 INFO @ Fri, 10 Dec 2021 12:50:12: 2000000 INFO @ Fri, 10 Dec 2021 12:50:15: 15000000 INFO @ Fri, 10 Dec 2021 12:50:16: 9000000 INFO @ Fri, 10 Dec 2021 12:50:17: 3000000 INFO @ Fri, 10 Dec 2021 12:50:20: 16000000 INFO @ Fri, 10 Dec 2021 12:50:21: 10000000 INFO @ Fri, 10 Dec 2021 12:50:22: 4000000 INFO @ Fri, 10 Dec 2021 12:50:25: 17000000 INFO @ Fri, 10 Dec 2021 12:50:26: 11000000 INFO @ Fri, 10 Dec 2021 12:50:27: 5000000 INFO @ Fri, 10 Dec 2021 12:50:30: 18000000 INFO @ Fri, 10 Dec 2021 12:50:31: 12000000 INFO @ Fri, 10 Dec 2021 12:50:32: 6000000 INFO @ Fri, 10 Dec 2021 12:50:35: 19000000 INFO @ Fri, 10 Dec 2021 12:50:36: 13000000 INFO @ Fri, 10 Dec 2021 12:50:37: 7000000 INFO @ Fri, 10 Dec 2021 12:50:41: 20000000 INFO @ Fri, 10 Dec 2021 12:50:41: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:50:41: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:50:41: #1 total tags in treatment: 20071617 INFO @ Fri, 10 Dec 2021 12:50:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:50:41: #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 12:50:41: 14000000 INFO @ Fri, 10 Dec 2021 12:50:42: #1 tags after filtering in treatment: 20071606 INFO @ Fri, 10 Dec 2021 12:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:50:42: #1 finished! INFO @ Fri, 10 Dec 2021 12:50:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:50:42: 8000000 INFO @ Fri, 10 Dec 2021 12:50:43: #2 number of paired peaks: 429 WARNING @ Fri, 10 Dec 2021 12:50:43: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Fri, 10 Dec 2021 12:50:43: start model_add_line... INFO @ Fri, 10 Dec 2021 12:50:43: start X-correlation... INFO @ Fri, 10 Dec 2021 12:50:43: end of X-cor INFO @ Fri, 10 Dec 2021 12:50:43: #2 finished! INFO @ Fri, 10 Dec 2021 12:50:43: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Dec 2021 12:50:43: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Dec 2021 12:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.05_model.r WARNING @ Fri, 10 Dec 2021 12:50:43: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:50:43: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Dec 2021 12:50:43: #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 12:50:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:50:46: 15000000 INFO @ Fri, 10 Dec 2021 12:50:47: 9000000 INFO @ Fri, 10 Dec 2021 12:50:51: 16000000 INFO @ Fri, 10 Dec 2021 12:50:52: 10000000 INFO @ Fri, 10 Dec 2021 12:50:56: 17000000 INFO @ Fri, 10 Dec 2021 12:50:57: 11000000 INFO @ Fri, 10 Dec 2021 12:51:01: 18000000 INFO @ Fri, 10 Dec 2021 12:51:02: 12000000 INFO @ Fri, 10 Dec 2021 12:51:06: 19000000 INFO @ Fri, 10 Dec 2021 12:51:07: 13000000 INFO @ Fri, 10 Dec 2021 12:51:11: 20000000 INFO @ Fri, 10 Dec 2021 12:51:12: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:51:12: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:51:12: #1 total tags in treatment: 20071617 INFO @ Fri, 10 Dec 2021 12:51:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:51:12: #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 12:51:12: 14000000 INFO @ Fri, 10 Dec 2021 12:51:13: #1 tags after filtering in treatment: 20071606 INFO @ Fri, 10 Dec 2021 12:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:51:13: #1 finished! INFO @ Fri, 10 Dec 2021 12:51:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:51:14: #2 number of paired peaks: 429 WARNING @ Fri, 10 Dec 2021 12:51:14: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Fri, 10 Dec 2021 12:51:14: start model_add_line... INFO @ Fri, 10 Dec 2021 12:51:14: start X-correlation... INFO @ Fri, 10 Dec 2021 12:51:14: end of X-cor INFO @ Fri, 10 Dec 2021 12:51:14: #2 finished! INFO @ Fri, 10 Dec 2021 12:51:14: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Dec 2021 12:51:14: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Dec 2021 12:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.10_model.r WARNING @ Fri, 10 Dec 2021 12:51:14: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:51:14: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Dec 2021 12:51:14: #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 12:51:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:51:17: 15000000 INFO @ Fri, 10 Dec 2021 12:51:20: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:51:22: 16000000 INFO @ Fri, 10 Dec 2021 12:51:28: 17000000 INFO @ Fri, 10 Dec 2021 12:51:33: 18000000 INFO @ Fri, 10 Dec 2021 12:51:37: 19000000 INFO @ Fri, 10 Dec 2021 12:51:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.05_summits.bed INFO @ Fri, 10 Dec 2021 12:51:39: Done! pass1 - making usageList (654 chroms): 4 millis pass2 - checking and writing primary data (21848 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:51:42: 20000000 INFO @ Fri, 10 Dec 2021 12:51:43: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:51:43: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:51:43: #1 total tags in treatment: 20071617 INFO @ Fri, 10 Dec 2021 12:51:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:51:43: #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 12:51:44: #1 tags after filtering in treatment: 20071606 INFO @ Fri, 10 Dec 2021 12:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:51:44: #1 finished! INFO @ Fri, 10 Dec 2021 12:51:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:51:45: #2 number of paired peaks: 429 WARNING @ Fri, 10 Dec 2021 12:51:45: Fewer paired peaks (429) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 429 pairs to build model! INFO @ Fri, 10 Dec 2021 12:51:45: start model_add_line... INFO @ Fri, 10 Dec 2021 12:51:45: start X-correlation... INFO @ Fri, 10 Dec 2021 12:51:45: end of X-cor INFO @ Fri, 10 Dec 2021 12:51:45: #2 finished! INFO @ Fri, 10 Dec 2021 12:51:45: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Dec 2021 12:51:45: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Dec 2021 12:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.20_model.r WARNING @ Fri, 10 Dec 2021 12:51:45: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:51:45: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Dec 2021 12:51:45: #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 12:51:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:51:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.10_summits.bed INFO @ Fri, 10 Dec 2021 12:52:11: Done! pass1 - making usageList (453 chroms): 1 millis pass2 - checking and writing primary data (5540 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:52:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712941/SRX4712941.20_summits.bed INFO @ Fri, 10 Dec 2021 12:52:40: Done! pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (1082 records, 4 fields): 10 millis CompletedMACS2peakCalling