Job ID = 14167156 SRX = SRX4712962 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13149824 spots for SRR7874092/SRR7874092.sra Written 13149824 spots for SRR7874092/SRR7874092.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167644 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:35 13149824 reads; of these: 13149824 (100.00%) were unpaired; of these: 404818 (3.08%) aligned 0 times 9407286 (71.54%) aligned exactly 1 time 3337720 (25.38%) aligned >1 times 96.92% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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_sort_core] merging from 8 files... [bam_rmdupse_core] 949592 / 12745006 = 0.0745 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 10:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.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 10:43:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:43:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:43:23: 1000000 INFO @ Fri, 10 Dec 2021 10:43:28: 2000000 INFO @ Fri, 10 Dec 2021 10:43:33: 3000000 INFO @ Fri, 10 Dec 2021 10:43:38: 4000000 INFO @ Fri, 10 Dec 2021 10:43:44: 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 10:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.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 10:43:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:43:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:43:49: 6000000 INFO @ Fri, 10 Dec 2021 10:43:53: 1000000 INFO @ Fri, 10 Dec 2021 10:43:54: 7000000 INFO @ Fri, 10 Dec 2021 10:43:58: 2000000 INFO @ Fri, 10 Dec 2021 10:43:59: 8000000 INFO @ Fri, 10 Dec 2021 10:44:03: 3000000 INFO @ Fri, 10 Dec 2021 10:44:05: 9000000 INFO @ Fri, 10 Dec 2021 10:44:09: 4000000 INFO @ Fri, 10 Dec 2021 10:44:10: 10000000 INFO @ Fri, 10 Dec 2021 10:44:15: 5000000 INFO @ Fri, 10 Dec 2021 10:44:15: 11000000 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 10:44:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.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 10:44:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:44:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:44:20: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:44:20: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:44:20: #1 total tags in treatment: 11795414 INFO @ Fri, 10 Dec 2021 10:44:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:44:20: #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 10:44:20: #1 tags after filtering in treatment: 11795414 INFO @ Fri, 10 Dec 2021 10:44:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:44:20: #1 finished! INFO @ Fri, 10 Dec 2021 10:44:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:44:20: 6000000 INFO @ Fri, 10 Dec 2021 10:44:21: #2 number of paired peaks: 274 WARNING @ Fri, 10 Dec 2021 10:44:21: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 10 Dec 2021 10:44:21: start model_add_line... INFO @ Fri, 10 Dec 2021 10:44:21: start X-correlation... INFO @ Fri, 10 Dec 2021 10:44:21: end of X-cor INFO @ Fri, 10 Dec 2021 10:44:21: #2 finished! INFO @ Fri, 10 Dec 2021 10:44:21: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 10:44:21: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 10:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.05_model.r WARNING @ Fri, 10 Dec 2021 10:44:21: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:44:21: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 10:44:21: #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 10:44:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:44:23: 1000000 INFO @ Fri, 10 Dec 2021 10:44:26: 7000000 INFO @ Fri, 10 Dec 2021 10:44:28: 2000000 INFO @ Fri, 10 Dec 2021 10:44:31: 8000000 INFO @ Fri, 10 Dec 2021 10:44:33: 3000000 INFO @ Fri, 10 Dec 2021 10:44:37: 9000000 INFO @ Fri, 10 Dec 2021 10:44:39: 4000000 INFO @ Fri, 10 Dec 2021 10:44:43: 10000000 INFO @ Fri, 10 Dec 2021 10:44:44: 5000000 INFO @ Fri, 10 Dec 2021 10:44:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:44:48: 11000000 INFO @ Fri, 10 Dec 2021 10:44:49: 6000000 INFO @ Fri, 10 Dec 2021 10:44:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:44:53: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:44:53: #1 total tags in treatment: 11795414 INFO @ Fri, 10 Dec 2021 10:44:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:44:53: #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 10:44:53: #1 tags after filtering in treatment: 11795414 INFO @ Fri, 10 Dec 2021 10:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:44:53: #1 finished! INFO @ Fri, 10 Dec 2021 10:44:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:44:54: #2 number of paired peaks: 274 WARNING @ Fri, 10 Dec 2021 10:44:54: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 10 Dec 2021 10:44:54: start model_add_line... INFO @ Fri, 10 Dec 2021 10:44:54: start X-correlation... INFO @ Fri, 10 Dec 2021 10:44:54: end of X-cor INFO @ Fri, 10 Dec 2021 10:44:54: #2 finished! INFO @ Fri, 10 Dec 2021 10:44:54: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 10:44:54: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 10:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.10_model.r WARNING @ Fri, 10 Dec 2021 10:44:54: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:44:54: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 10:44:54: #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 10:44:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:44:55: 7000000 INFO @ Fri, 10 Dec 2021 10:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.05_summits.bed INFO @ Fri, 10 Dec 2021 10:44:58: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1539 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:45:00: 8000000 INFO @ Fri, 10 Dec 2021 10:45:06: 9000000 INFO @ Fri, 10 Dec 2021 10:45:11: 10000000 INFO @ Fri, 10 Dec 2021 10:45:16: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:45:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:45:20: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:45:20: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:45:20: #1 total tags in treatment: 11795414 INFO @ Fri, 10 Dec 2021 10:45:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:45:20: #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 10:45:21: #1 tags after filtering in treatment: 11795414 INFO @ Fri, 10 Dec 2021 10:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:45:21: #1 finished! INFO @ Fri, 10 Dec 2021 10:45:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:45:22: #2 number of paired peaks: 274 WARNING @ Fri, 10 Dec 2021 10:45:22: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Fri, 10 Dec 2021 10:45:22: start model_add_line... INFO @ Fri, 10 Dec 2021 10:45:22: start X-correlation... INFO @ Fri, 10 Dec 2021 10:45:22: end of X-cor INFO @ Fri, 10 Dec 2021 10:45:22: #2 finished! INFO @ Fri, 10 Dec 2021 10:45:22: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 10:45:22: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 10:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.20_model.r WARNING @ Fri, 10 Dec 2021 10:45:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:45:22: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 10:45:22: #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 10:45:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.10_summits.bed INFO @ Fri, 10 Dec 2021 10:45:30: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1232 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:45:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712962/SRX4712962.20_summits.bed INFO @ Fri, 10 Dec 2021 10:45:58: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 2 millis CompletedMACS2peakCalling