Job ID = 14170397 SRX = SRX8689018 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7306574 spots for SRR12174274/SRR12174274.sra Written 7306574 spots for SRR12174274/SRR12174274.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170803 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:45 7306574 reads; of these: 7306574 (100.00%) were unpaired; of these: 333778 (4.57%) aligned 0 times 4770270 (65.29%) aligned exactly 1 time 2202526 (30.14%) aligned >1 times 95.43% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 380264 / 6972796 = 0.0545 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 06:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.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 06:46:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:46:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:46:38: 1000000 INFO @ Sat, 11 Dec 2021 06:46:44: 2000000 INFO @ Sat, 11 Dec 2021 06:46:49: 3000000 INFO @ Sat, 11 Dec 2021 06:46:55: 4000000 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 06:47:00: 5000000 INFO @ Sat, 11 Dec 2021 06:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.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 06:47:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:07: 6000000 INFO @ Sat, 11 Dec 2021 06:47:10: 1000000 INFO @ Sat, 11 Dec 2021 06:47:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:11: #1 total tags in treatment: 6592532 INFO @ Sat, 11 Dec 2021 06:47:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:11: #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 06:47:11: #1 tags after filtering in treatment: 6592532 INFO @ Sat, 11 Dec 2021 06:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:11: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:11: #2 number of paired peaks: 404 WARNING @ Sat, 11 Dec 2021 06:47:11: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:11: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:11: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:11: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:11: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:11: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 06:47:11: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 11 Dec 2021 06:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.05_model.r WARNING @ Sat, 11 Dec 2021 06:47:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:11: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 11 Dec 2021 06:47:11: #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 06:47:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:17: 2000000 INFO @ Sat, 11 Dec 2021 06:47:23: 3000000 INFO @ Sat, 11 Dec 2021 06:47:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:28: 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 @ Sat, 11 Dec 2021 06:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.05_summits.bed INFO @ Sat, 11 Dec 2021 06:47:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1476 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.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 06:47:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:34: 5000000 INFO @ Sat, 11 Dec 2021 06:47:40: 1000000 INFO @ Sat, 11 Dec 2021 06:47:41: 6000000 INFO @ Sat, 11 Dec 2021 06:47:45: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:45: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:45: #1 total tags in treatment: 6592532 INFO @ Sat, 11 Dec 2021 06:47:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:45: #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 06:47:45: #1 tags after filtering in treatment: 6592532 INFO @ Sat, 11 Dec 2021 06:47:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:45: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:46: #2 number of paired peaks: 404 WARNING @ Sat, 11 Dec 2021 06:47:46: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:46: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:46: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:46: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:46: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:46: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 06:47:46: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 11 Dec 2021 06:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.10_model.r WARNING @ Sat, 11 Dec 2021 06:47:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:46: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 11 Dec 2021 06:47:46: #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 06:47:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:47: 2000000 INFO @ Sat, 11 Dec 2021 06:47:54: 3000000 INFO @ Sat, 11 Dec 2021 06:47:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:48:01: 4000000 INFO @ Sat, 11 Dec 2021 06:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.10_summits.bed INFO @ Sat, 11 Dec 2021 06:48:06: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1221 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:09: 5000000 INFO @ Sat, 11 Dec 2021 06:48:16: 6000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:48:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:20: #1 total tags in treatment: 6592532 INFO @ Sat, 11 Dec 2021 06:48:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:20: #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 06:48:20: #1 tags after filtering in treatment: 6592532 INFO @ Sat, 11 Dec 2021 06:48:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:20: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:21: #2 number of paired peaks: 404 WARNING @ Sat, 11 Dec 2021 06:48:21: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Sat, 11 Dec 2021 06:48:21: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:21: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:21: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:21: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:21: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 06:48:21: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 11 Dec 2021 06:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.20_model.r WARNING @ Sat, 11 Dec 2021 06:48:21: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:48:21: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 11 Dec 2021 06:48:21: #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 06:48:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:48:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689018/SRX8689018.20_summits.bed INFO @ Sat, 11 Dec 2021 06:48:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (895 records, 4 fields): 3 millis CompletedMACS2peakCalling