Job ID = 14167137 SRX = SRX4712953 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33027501 spots for SRR7874083/SRR7874083.sra Written 33027501 spots for SRR7874083/SRR7874083.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167615 ("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: 00:09:39 33027501 reads; of these: 33027501 (100.00%) were unpaired; of these: 1945644 (5.89%) aligned 0 times 23363971 (70.74%) aligned exactly 1 time 7717886 (23.37%) aligned >1 times 94.11% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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 16 files... [bam_rmdupse_core] 22571453 / 31081857 = 0.7262 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 10:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.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 10:38:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:38:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:38:52: 1000000 INFO @ Fri, 10 Dec 2021 10:38:57: 2000000 INFO @ Fri, 10 Dec 2021 10:39:02: 3000000 INFO @ Fri, 10 Dec 2021 10:39:08: 4000000 INFO @ Fri, 10 Dec 2021 10:39:13: 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 10:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.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 10:39:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:39:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:39:19: 6000000 INFO @ Fri, 10 Dec 2021 10:39:23: 1000000 INFO @ Fri, 10 Dec 2021 10:39:25: 7000000 INFO @ Fri, 10 Dec 2021 10:39:30: 2000000 INFO @ Fri, 10 Dec 2021 10:39:31: 8000000 INFO @ Fri, 10 Dec 2021 10:39:34: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:39:34: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:39:34: #1 total tags in treatment: 8510404 INFO @ Fri, 10 Dec 2021 10:39:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:39:34: #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 10:39:34: #1 tags after filtering in treatment: 8510404 INFO @ Fri, 10 Dec 2021 10:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:39:34: #1 finished! INFO @ Fri, 10 Dec 2021 10:39:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:39:34: #2 number of paired peaks: 897 WARNING @ Fri, 10 Dec 2021 10:39:34: Fewer paired peaks (897) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 897 pairs to build model! INFO @ Fri, 10 Dec 2021 10:39:34: start model_add_line... INFO @ Fri, 10 Dec 2021 10:39:34: start X-correlation... INFO @ Fri, 10 Dec 2021 10:39:34: end of X-cor INFO @ Fri, 10 Dec 2021 10:39:34: #2 finished! INFO @ Fri, 10 Dec 2021 10:39:34: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Dec 2021 10:39:34: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Dec 2021 10:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.05_model.r WARNING @ Fri, 10 Dec 2021 10:39:34: #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 10:39:34: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Dec 2021 10:39:34: #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 10:39:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:39:36: 3000000 INFO @ Fri, 10 Dec 2021 10:39:43: 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 @ Fri, 10 Dec 2021 10:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.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 10:39:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:39:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:39:49: 5000000 INFO @ Fri, 10 Dec 2021 10:39:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:39:52: 1000000 INFO @ Fri, 10 Dec 2021 10:39:56: 6000000 INFO @ Fri, 10 Dec 2021 10:39:59: 2000000 INFO @ Fri, 10 Dec 2021 10:40:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.05_summits.bed INFO @ Fri, 10 Dec 2021 10:40:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6613 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:40:02: 7000000 INFO @ Fri, 10 Dec 2021 10:40:05: 3000000 INFO @ Fri, 10 Dec 2021 10:40:09: 8000000 INFO @ Fri, 10 Dec 2021 10:40:11: 4000000 INFO @ Fri, 10 Dec 2021 10:40:12: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:40:12: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:40:12: #1 total tags in treatment: 8510404 INFO @ Fri, 10 Dec 2021 10:40:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:40:12: #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 10:40:12: #1 tags after filtering in treatment: 8510404 INFO @ Fri, 10 Dec 2021 10:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:40:12: #1 finished! INFO @ Fri, 10 Dec 2021 10:40:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:40:13: #2 number of paired peaks: 897 WARNING @ Fri, 10 Dec 2021 10:40:13: Fewer paired peaks (897) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 897 pairs to build model! INFO @ Fri, 10 Dec 2021 10:40:13: start model_add_line... INFO @ Fri, 10 Dec 2021 10:40:13: start X-correlation... INFO @ Fri, 10 Dec 2021 10:40:13: end of X-cor INFO @ Fri, 10 Dec 2021 10:40:13: #2 finished! INFO @ Fri, 10 Dec 2021 10:40:13: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Dec 2021 10:40:13: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Dec 2021 10:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.10_model.r WARNING @ Fri, 10 Dec 2021 10:40:13: #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 10:40:13: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Dec 2021 10:40:13: #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 10:40:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:40:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:40:17: 5000000 INFO @ Fri, 10 Dec 2021 10:40:22: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:40:28: 7000000 INFO @ Fri, 10 Dec 2021 10:40:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:40:34: 8000000 INFO @ Fri, 10 Dec 2021 10:40:37: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:40:37: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:40:37: #1 total tags in treatment: 8510404 INFO @ Fri, 10 Dec 2021 10:40:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:40:37: #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 10:40:37: #1 tags after filtering in treatment: 8510404 INFO @ Fri, 10 Dec 2021 10:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:40:37: #1 finished! INFO @ Fri, 10 Dec 2021 10:40:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:40:37: #2 number of paired peaks: 897 WARNING @ Fri, 10 Dec 2021 10:40:37: Fewer paired peaks (897) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 897 pairs to build model! INFO @ Fri, 10 Dec 2021 10:40:37: start model_add_line... INFO @ Fri, 10 Dec 2021 10:40:38: start X-correlation... INFO @ Fri, 10 Dec 2021 10:40:38: end of X-cor INFO @ Fri, 10 Dec 2021 10:40:38: #2 finished! INFO @ Fri, 10 Dec 2021 10:40:38: #2 predicted fragment length is 99 bps INFO @ Fri, 10 Dec 2021 10:40:38: #2 alternative fragment length(s) may be 99 bps INFO @ Fri, 10 Dec 2021 10:40:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.20_model.r WARNING @ Fri, 10 Dec 2021 10:40:38: #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 10:40:38: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Fri, 10 Dec 2021 10:40:38: #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 10:40:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:40:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:40:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:40:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:40:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.10_summits.bed INFO @ Fri, 10 Dec 2021 10:40:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3399 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:40:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:41:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:41:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:41:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712953/SRX4712953.20_summits.bed INFO @ Fri, 10 Dec 2021 10:41:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1998 records, 4 fields): 4 millis CompletedMACS2peakCalling