Job ID = 14167243 SRX = SRX8688908 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9108074 spots for SRR12174260/SRR12174260.sra Written 9108074 spots for SRR12174260/SRR12174260.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167822 ("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: 00:04:02 9108074 reads; of these: 9108074 (100.00%) were unpaired; of these: 622537 (6.84%) aligned 0 times 5487306 (60.25%) aligned exactly 1 time 2998231 (32.92%) aligned >1 times 93.16% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 620352 / 8485537 = 0.0731 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 11:23:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.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 11:23:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:23:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:23:09: 1000000 INFO @ Fri, 10 Dec 2021 11:23:15: 2000000 INFO @ Fri, 10 Dec 2021 11:23:22: 3000000 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 11:23:28: 4000000 INFO @ Fri, 10 Dec 2021 11:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.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 11:23:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:23:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:23:35: 5000000 INFO @ Fri, 10 Dec 2021 11:23:38: 1000000 INFO @ Fri, 10 Dec 2021 11:23:42: 6000000 INFO @ Fri, 10 Dec 2021 11:23:45: 2000000 INFO @ Fri, 10 Dec 2021 11:23:48: 7000000 INFO @ Fri, 10 Dec 2021 11:23:52: 3000000 INFO @ Fri, 10 Dec 2021 11:23:55: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:23:55: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:23:55: #1 total tags in treatment: 7865185 INFO @ Fri, 10 Dec 2021 11:23:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:23:55: #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 11:23:55: #1 tags after filtering in treatment: 7865185 INFO @ Fri, 10 Dec 2021 11:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:23:55: #1 finished! INFO @ Fri, 10 Dec 2021 11:23:55: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:23:56: #2 number of paired peaks: 422 WARNING @ Fri, 10 Dec 2021 11:23:56: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 10 Dec 2021 11:23:56: start model_add_line... INFO @ Fri, 10 Dec 2021 11:23:56: start X-correlation... INFO @ Fri, 10 Dec 2021 11:23:56: end of X-cor INFO @ Fri, 10 Dec 2021 11:23:56: #2 finished! INFO @ Fri, 10 Dec 2021 11:23:56: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:23:56: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.05_model.r WARNING @ Fri, 10 Dec 2021 11:23:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:23:56: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:23:56: #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 11:23:56: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:23:56: #3 Pre-compute pvalue-qvalue table... 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 11:23:59: 4000000 INFO @ Fri, 10 Dec 2021 11:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.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 11:24:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:24:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:24:06: 5000000 INFO @ Fri, 10 Dec 2021 11:24:08: 1000000 INFO @ Fri, 10 Dec 2021 11:24:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:13: 6000000 INFO @ Fri, 10 Dec 2021 11:24:15: 2000000 INFO @ Fri, 10 Dec 2021 11:24:21: 7000000 INFO @ Fri, 10 Dec 2021 11:24:21: 3000000 INFO @ Fri, 10 Dec 2021 11:24:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.05_summits.bed INFO @ Fri, 10 Dec 2021 11:24:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1710 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:24:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:24:27: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:24:27: #1 total tags in treatment: 7865185 INFO @ Fri, 10 Dec 2021 11:24:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:27: #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 11:24:27: #1 tags after filtering in treatment: 7865185 INFO @ Fri, 10 Dec 2021 11:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:24:27: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:27: #2 number of paired peaks: 422 WARNING @ Fri, 10 Dec 2021 11:24:27: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 10 Dec 2021 11:24:27: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:28: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:28: 4000000 INFO @ Fri, 10 Dec 2021 11:24:28: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:28: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:28: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:24:28: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.10_model.r WARNING @ Fri, 10 Dec 2021 11:24:28: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:24:28: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:24:28: #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 11:24:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:34: 5000000 INFO @ Fri, 10 Dec 2021 11:24:40: 6000000 INFO @ Fri, 10 Dec 2021 11:24:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:24:47: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:24:52: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:24:52: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:24:52: #1 total tags in treatment: 7865185 INFO @ Fri, 10 Dec 2021 11:24:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:24:52: #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 11:24:53: #1 tags after filtering in treatment: 7865185 INFO @ Fri, 10 Dec 2021 11:24:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:24:53: #1 finished! INFO @ Fri, 10 Dec 2021 11:24:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:24:53: #2 number of paired peaks: 422 WARNING @ Fri, 10 Dec 2021 11:24:53: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 10 Dec 2021 11:24:53: start model_add_line... INFO @ Fri, 10 Dec 2021 11:24:53: start X-correlation... INFO @ Fri, 10 Dec 2021 11:24:54: end of X-cor INFO @ Fri, 10 Dec 2021 11:24:54: #2 finished! INFO @ Fri, 10 Dec 2021 11:24:54: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 11:24:54: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 11:24:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.20_model.r WARNING @ Fri, 10 Dec 2021 11:24:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:24:54: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 11:24:54: #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 11:24:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:24:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.10_summits.bed INFO @ Fri, 10 Dec 2021 11:24:54: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1362 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:25:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:25:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:25:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:25:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688908/SRX8688908.20_summits.bed INFO @ Fri, 10 Dec 2021 11:25:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 3 millis CompletedMACS2peakCalling