Job ID = 16438943 SRX = SRX13227902 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25039051 spots for SRR17038015/SRR17038015.sra Written 25039051 spots for SRR17038015/SRR17038015.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439157 ("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: 00:18:45 25039051 reads; of these: 25039051 (100.00%) were unpaired; of these: 867880 (3.47%) aligned 0 times 14016152 (55.98%) aligned exactly 1 time 10155019 (40.56%) aligned >1 times 96.53% overall alignment rate Time searching: 00:18:45 Overall time: 00:18:46 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 12 files... [bam_rmdupse_core] 13311821 / 24171171 = 0.5507 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.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 @ Tue, 02 Aug 2022 14:40:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:40:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:40:36: 1000000 INFO @ Tue, 02 Aug 2022 14:40:44: 2000000 INFO @ Tue, 02 Aug 2022 14:40:52: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.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 @ Tue, 02 Aug 2022 14:40:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:40:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:00: 4000000 INFO @ Tue, 02 Aug 2022 14:41:06: 1000000 INFO @ Tue, 02 Aug 2022 14:41:09: 5000000 INFO @ Tue, 02 Aug 2022 14:41:15: 2000000 INFO @ Tue, 02 Aug 2022 14:41:17: 6000000 INFO @ Tue, 02 Aug 2022 14:41:23: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:41:25: 7000000 INFO @ Tue, 02 Aug 2022 14:41:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.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 @ Tue, 02 Aug 2022 14:41:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:31: 4000000 INFO @ Tue, 02 Aug 2022 14:41:34: 8000000 INFO @ Tue, 02 Aug 2022 14:41:37: 1000000 INFO @ Tue, 02 Aug 2022 14:41:40: 5000000 INFO @ Tue, 02 Aug 2022 14:41:42: 9000000 INFO @ Tue, 02 Aug 2022 14:41:47: 2000000 INFO @ Tue, 02 Aug 2022 14:41:48: 6000000 INFO @ Tue, 02 Aug 2022 14:41:50: 10000000 INFO @ Tue, 02 Aug 2022 14:41:56: 3000000 INFO @ Tue, 02 Aug 2022 14:41:56: 7000000 INFO @ Tue, 02 Aug 2022 14:41:58: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:41:58: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:41:58: #1 total tags in treatment: 10859350 INFO @ Tue, 02 Aug 2022 14:41:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:41:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:41:58: #1 tags after filtering in treatment: 10859350 INFO @ Tue, 02 Aug 2022 14:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:41:58: #1 finished! INFO @ Tue, 02 Aug 2022 14:41:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:41:59: #2 number of paired peaks: 494 WARNING @ Tue, 02 Aug 2022 14:41:59: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Tue, 02 Aug 2022 14:41:59: start model_add_line... INFO @ Tue, 02 Aug 2022 14:41:59: start X-correlation... INFO @ Tue, 02 Aug 2022 14:41:59: end of X-cor INFO @ Tue, 02 Aug 2022 14:41:59: #2 finished! INFO @ Tue, 02 Aug 2022 14:41:59: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 14:41:59: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 14:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.05_model.r WARNING @ Tue, 02 Aug 2022 14:41:59: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:41:59: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 14:41:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:41:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:04: 4000000 INFO @ Tue, 02 Aug 2022 14:42:05: 8000000 INFO @ Tue, 02 Aug 2022 14:42:12: 5000000 INFO @ Tue, 02 Aug 2022 14:42:13: 9000000 INFO @ Tue, 02 Aug 2022 14:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:21: 6000000 INFO @ Tue, 02 Aug 2022 14:42:22: 10000000 INFO @ Tue, 02 Aug 2022 14:42:29: 7000000 INFO @ Tue, 02 Aug 2022 14:42:29: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:42:29: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:42:29: #1 total tags in treatment: 10859350 INFO @ Tue, 02 Aug 2022 14:42:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:42:29: #1 tags after filtering in treatment: 10859350 INFO @ Tue, 02 Aug 2022 14:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:29: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:30: #2 number of paired peaks: 494 WARNING @ Tue, 02 Aug 2022 14:42:30: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Tue, 02 Aug 2022 14:42:30: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:30: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:30: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 14:42:30: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 14:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.10_model.r WARNING @ Tue, 02 Aug 2022 14:42:30: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:30: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 14:42:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:42:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.05_summits.bed INFO @ Tue, 02 Aug 2022 14:42:34: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7289 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:42:37: 8000000 INFO @ Tue, 02 Aug 2022 14:42:45: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:42:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:42:53: 10000000 INFO @ Tue, 02 Aug 2022 14:42:59: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:42:59: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:42:59: #1 total tags in treatment: 10859350 INFO @ Tue, 02 Aug 2022 14:42:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:43:00: #1 tags after filtering in treatment: 10859350 INFO @ Tue, 02 Aug 2022 14:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:43:00: #1 finished! INFO @ Tue, 02 Aug 2022 14:43:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:43:00: #2 number of paired peaks: 494 WARNING @ Tue, 02 Aug 2022 14:43:00: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Tue, 02 Aug 2022 14:43:00: start model_add_line... INFO @ Tue, 02 Aug 2022 14:43:00: start X-correlation... INFO @ Tue, 02 Aug 2022 14:43:00: end of X-cor INFO @ Tue, 02 Aug 2022 14:43:00: #2 finished! INFO @ Tue, 02 Aug 2022 14:43:00: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 14:43:00: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 14:43:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.20_model.r WARNING @ Tue, 02 Aug 2022 14:43:00: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:43:00: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 14:43:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:43:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:43:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:43:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.10_summits.bed INFO @ Tue, 02 Aug 2022 14:43:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3548 records, 4 fields): 91 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:43:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX13227902/SRX13227902.20_summits.bed INFO @ Tue, 02 Aug 2022 14:43:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1239 records, 4 fields): 40 millis CompletedMACS2peakCalling