Job ID = 14171102 SRX = SRX9063532 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12666368 spots for SRR12576657/SRR12576657.sra Written 12666368 spots for SRR12576657/SRR12576657.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171549 ("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: 00:05:34 12666368 reads; of these: 12666368 (100.00%) were unpaired; of these: 475568 (3.75%) aligned 0 times 9113288 (71.95%) aligned exactly 1 time 3077512 (24.30%) aligned >1 times 96.25% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 2585838 / 12190800 = 0.2121 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 09:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.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 09:42:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:42:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:42:54: 1000000 INFO @ Sat, 11 Dec 2021 09:43:00: 2000000 INFO @ Sat, 11 Dec 2021 09:43:06: 3000000 INFO @ Sat, 11 Dec 2021 09:43:12: 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 09:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.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 09:43:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:18: 5000000 INFO @ Sat, 11 Dec 2021 09:43:25: 1000000 INFO @ Sat, 11 Dec 2021 09:43:26: 6000000 INFO @ Sat, 11 Dec 2021 09:43:33: 2000000 INFO @ Sat, 11 Dec 2021 09:43:33: 7000000 INFO @ Sat, 11 Dec 2021 09:43:40: 3000000 INFO @ Sat, 11 Dec 2021 09:43:40: 8000000 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 09:43:47: 4000000 INFO @ Sat, 11 Dec 2021 09:43:47: 9000000 INFO @ Sat, 11 Dec 2021 09:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.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 09:43:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:43:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:43:52: #1 tag size is determined as 76 bps INFO @ Sat, 11 Dec 2021 09:43:52: #1 tag size = 76 INFO @ Sat, 11 Dec 2021 09:43:52: #1 total tags in treatment: 9604962 INFO @ Sat, 11 Dec 2021 09:43:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:43:52: #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 09:43:52: #1 tags after filtering in treatment: 9604962 INFO @ Sat, 11 Dec 2021 09:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:43:52: #1 finished! INFO @ Sat, 11 Dec 2021 09:43:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:43:52: #2 number of paired peaks: 112 WARNING @ Sat, 11 Dec 2021 09:43:52: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 11 Dec 2021 09:43:52: start model_add_line... INFO @ Sat, 11 Dec 2021 09:43:53: start X-correlation... INFO @ Sat, 11 Dec 2021 09:43:53: end of X-cor INFO @ Sat, 11 Dec 2021 09:43:53: #2 finished! INFO @ Sat, 11 Dec 2021 09:43:53: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 09:43:53: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 09:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.05_model.r WARNING @ Sat, 11 Dec 2021 09:43:53: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:43:53: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 09:43:53: #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 09:43:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:43:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:43:55: 5000000 INFO @ Sat, 11 Dec 2021 09:43:55: 1000000 INFO @ Sat, 11 Dec 2021 09:44:02: 6000000 INFO @ Sat, 11 Dec 2021 09:44:02: 2000000 INFO @ Sat, 11 Dec 2021 09:44:09: 7000000 INFO @ Sat, 11 Dec 2021 09:44:09: 3000000 INFO @ Sat, 11 Dec 2021 09:44:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:17: 8000000 INFO @ Sat, 11 Dec 2021 09:44:17: 4000000 INFO @ Sat, 11 Dec 2021 09:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.05_summits.bed INFO @ Sat, 11 Dec 2021 09:44:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:44:24: 5000000 INFO @ Sat, 11 Dec 2021 09:44:24: 9000000 INFO @ Sat, 11 Dec 2021 09:44:28: #1 tag size is determined as 76 bps INFO @ Sat, 11 Dec 2021 09:44:28: #1 tag size = 76 INFO @ Sat, 11 Dec 2021 09:44:28: #1 total tags in treatment: 9604962 INFO @ Sat, 11 Dec 2021 09:44:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:28: #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 09:44:28: #1 tags after filtering in treatment: 9604962 INFO @ Sat, 11 Dec 2021 09:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:44:28: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:29: #2 number of paired peaks: 112 WARNING @ Sat, 11 Dec 2021 09:44:29: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 11 Dec 2021 09:44:29: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:29: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:29: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:29: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:29: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 09:44:29: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 09:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.10_model.r WARNING @ Sat, 11 Dec 2021 09:44:29: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:44:29: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 09:44:29: #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 09:44:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:44:31: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:44:37: 7000000 INFO @ Sat, 11 Dec 2021 09:44:44: 8000000 INFO @ Sat, 11 Dec 2021 09:44:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:44:50: 9000000 INFO @ Sat, 11 Dec 2021 09:44:54: #1 tag size is determined as 76 bps INFO @ Sat, 11 Dec 2021 09:44:54: #1 tag size = 76 INFO @ Sat, 11 Dec 2021 09:44:54: #1 total tags in treatment: 9604962 INFO @ Sat, 11 Dec 2021 09:44:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:44:54: #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 09:44:54: #1 tags after filtering in treatment: 9604962 INFO @ Sat, 11 Dec 2021 09:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:44:54: #1 finished! INFO @ Sat, 11 Dec 2021 09:44:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:44:55: #2 number of paired peaks: 112 WARNING @ Sat, 11 Dec 2021 09:44:55: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 11 Dec 2021 09:44:55: start model_add_line... INFO @ Sat, 11 Dec 2021 09:44:55: start X-correlation... INFO @ Sat, 11 Dec 2021 09:44:55: end of X-cor INFO @ Sat, 11 Dec 2021 09:44:55: #2 finished! INFO @ Sat, 11 Dec 2021 09:44:55: #2 predicted fragment length is 84 bps INFO @ Sat, 11 Dec 2021 09:44:55: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 11 Dec 2021 09:44:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.20_model.r WARNING @ Sat, 11 Dec 2021 09:44:55: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:44:55: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 11 Dec 2021 09:44:55: #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 09:44:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:44:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.10_summits.bed INFO @ Sat, 11 Dec 2021 09:44:58: Done! BigWig に変換しました。 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (809 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:45:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9063532/SRX9063532.20_summits.bed INFO @ Sat, 11 Dec 2021 09:45:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling