Job ID = 10165837 SRX = SRX7723687 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26497225 spots for SRR11084643/SRR11084643.sra Written 26497225 spots for SRR11084643/SRR11084643.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166308 ("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: 00:21:16 26497225 reads; of these: 26497225 (100.00%) were unpaired; of these: 3394683 (12.81%) aligned 0 times 13060864 (49.29%) aligned exactly 1 time 10041678 (37.90%) aligned >1 times 87.19% overall alignment rate Time searching: 00:21:16 Overall time: 00:21:16 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] 12651048 / 23102542 = 0.5476 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.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 @ Thu, 08 Oct 2020 20:25:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:25:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:25:56: 1000000 INFO @ Thu, 08 Oct 2020 20:26:01: 2000000 INFO @ Thu, 08 Oct 2020 20:26:07: 3000000 INFO @ Thu, 08 Oct 2020 20:26:13: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:26:19: 5000000 INFO @ Thu, 08 Oct 2020 20:26:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.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 @ Thu, 08 Oct 2020 20:26:20: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:26:20: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:26:26: 6000000 INFO @ Thu, 08 Oct 2020 20:26:26: 1000000 INFO @ Thu, 08 Oct 2020 20:26:32: 7000000 INFO @ Thu, 08 Oct 2020 20:26:33: 2000000 INFO @ Thu, 08 Oct 2020 20:26:39: 8000000 INFO @ Thu, 08 Oct 2020 20:26:40: 3000000 INFO @ Thu, 08 Oct 2020 20:26:46: 9000000 INFO @ Thu, 08 Oct 2020 20:26:47: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.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 @ Thu, 08 Oct 2020 20:26:50: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:26:50: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:26:53: 10000000 INFO @ Thu, 08 Oct 2020 20:26:54: 5000000 INFO @ Thu, 08 Oct 2020 20:26:56: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:26:56: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:26:56: #1 total tags in treatment: 10451494 INFO @ Thu, 08 Oct 2020 20:26:56: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:26:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:26:56: #1 tags after filtering in treatment: 10451494 INFO @ Thu, 08 Oct 2020 20:26:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:26:56: #1 finished! INFO @ Thu, 08 Oct 2020 20:26:56: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:26:57: #2 number of paired peaks: 484 WARNING @ Thu, 08 Oct 2020 20:26:57: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Thu, 08 Oct 2020 20:26:57: start model_add_line... INFO @ Thu, 08 Oct 2020 20:26:57: start X-correlation... INFO @ Thu, 08 Oct 2020 20:26:57: end of X-cor INFO @ Thu, 08 Oct 2020 20:26:57: #2 finished! INFO @ Thu, 08 Oct 2020 20:26:57: #2 predicted fragment length is 66 bps INFO @ Thu, 08 Oct 2020 20:26:57: #2 alternative fragment length(s) may be 66 bps INFO @ Thu, 08 Oct 2020 20:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_model.r WARNING @ Thu, 08 Oct 2020 20:26:57: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:26:57: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Thu, 08 Oct 2020 20:26:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:26:57: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:26:58: 1000000 INFO @ Thu, 08 Oct 2020 20:27:02: 6000000 INFO @ Thu, 08 Oct 2020 20:27:07: 2000000 INFO @ Thu, 08 Oct 2020 20:27:09: 7000000 INFO @ Thu, 08 Oct 2020 20:27:15: 3000000 INFO @ Thu, 08 Oct 2020 20:27:17: 8000000 INFO @ Thu, 08 Oct 2020 20:27:19: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:24: 4000000 INFO @ Thu, 08 Oct 2020 20:27:24: 9000000 INFO @ Thu, 08 Oct 2020 20:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_summits.bed INFO @ Thu, 08 Oct 2020 20:27:30: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3029 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:27:32: 10000000 INFO @ Thu, 08 Oct 2020 20:27:32: 5000000 INFO @ Thu, 08 Oct 2020 20:27:35: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:27:35: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:27:35: #1 total tags in treatment: 10451494 INFO @ Thu, 08 Oct 2020 20:27:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:27:35: #1 tags after filtering in treatment: 10451494 INFO @ Thu, 08 Oct 2020 20:27:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:36: #2 number of paired peaks: 484 WARNING @ Thu, 08 Oct 2020 20:27:36: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Thu, 08 Oct 2020 20:27:36: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:36: #2 predicted fragment length is 66 bps INFO @ Thu, 08 Oct 2020 20:27:36: #2 alternative fragment length(s) may be 66 bps INFO @ Thu, 08 Oct 2020 20:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_model.r WARNING @ Thu, 08 Oct 2020 20:27:36: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:27:36: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Thu, 08 Oct 2020 20:27:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:27:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:27:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:27:48: 7000000 INFO @ Thu, 08 Oct 2020 20:27:56: 8000000 INFO @ Thu, 08 Oct 2020 20:27:58: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:04: 9000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:28:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_summits.bed INFO @ Thu, 08 Oct 2020 20:28:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1789 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:28:11: 10000000 INFO @ Thu, 08 Oct 2020 20:28:15: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:28:15: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:28:15: #1 total tags in treatment: 10451494 INFO @ Thu, 08 Oct 2020 20:28:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:28:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:28:15: #1 tags after filtering in treatment: 10451494 INFO @ Thu, 08 Oct 2020 20:28:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:28:15: #1 finished! INFO @ Thu, 08 Oct 2020 20:28:15: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:28:16: #2 number of paired peaks: 484 WARNING @ Thu, 08 Oct 2020 20:28:16: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Thu, 08 Oct 2020 20:28:16: start model_add_line... INFO @ Thu, 08 Oct 2020 20:28:16: start X-correlation... INFO @ Thu, 08 Oct 2020 20:28:16: end of X-cor INFO @ Thu, 08 Oct 2020 20:28:16: #2 finished! INFO @ Thu, 08 Oct 2020 20:28:16: #2 predicted fragment length is 66 bps INFO @ Thu, 08 Oct 2020 20:28:16: #2 alternative fragment length(s) may be 66 bps INFO @ Thu, 08 Oct 2020 20:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_model.r WARNING @ Thu, 08 Oct 2020 20:28:16: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:28:16: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Thu, 08 Oct 2020 20:28:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:28:16: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:28:37: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_summits.bed INFO @ Thu, 08 Oct 2020 20:28:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1115 records, 4 fields): 3 millis CompletedMACS2peakCalling