Job ID = 12265952 SRX = SRX7282591 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17208 spots for SRR10603126/SRR10603126.sra Written 17208 spots for SRR10603126/SRR10603126.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266056 ("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: 00:00:01 17208 reads; of these: 17208 (100.00%) were unpaired; of these: 2546 (14.80%) aligned 0 times 6554 (38.09%) aligned exactly 1 time 8108 (47.12%) aligned >1 times 85.20% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 9812 / 14662 = 0.6692 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:38:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.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, 03 Apr 2021 08:38:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:38:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:38:58: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:38:58: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:38:58: #1 total tags in treatment: 4850 INFO @ Sat, 03 Apr 2021 08:38:58: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:38:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:38:58: #1 tags after filtering in treatment: 4849 INFO @ Sat, 03 Apr 2021 08:38:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:38:58: #1 finished! INFO @ Sat, 03 Apr 2021 08:38:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:38:58: #2 number of paired peaks: 145 WARNING @ Sat, 03 Apr 2021 08:38:58: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 03 Apr 2021 08:38:58: start model_add_line... INFO @ Sat, 03 Apr 2021 08:38:58: start X-correlation... INFO @ Sat, 03 Apr 2021 08:38:58: end of X-cor INFO @ Sat, 03 Apr 2021 08:38:58: #2 finished! INFO @ Sat, 03 Apr 2021 08:38:58: #2 predicted fragment length is 10 bps INFO @ Sat, 03 Apr 2021 08:38:58: #2 alternative fragment length(s) may be 10,45,79,114,145,155,176,188,225,265,299,335,364,520 bps INFO @ Sat, 03 Apr 2021 08:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.05_model.r WARNING @ Sat, 03 Apr 2021 08:38:58: #2 Since the d (10) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:38:58: #2 You may need to consider one of the other alternative d(s): 10,45,79,114,145,155,176,188,225,265,299,335,364,520 WARNING @ Sat, 03 Apr 2021 08:38:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:38:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:38:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:38:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:38:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:38:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.05_summits.bed INFO @ Sat, 03 Apr 2021 08:38:58: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.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, 03 Apr 2021 08:39:28: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:39:28: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:39:28: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:39:28: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:39:28: #1 total tags in treatment: 4850 INFO @ Sat, 03 Apr 2021 08:39:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:39:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:39:28: #1 tags after filtering in treatment: 4849 INFO @ Sat, 03 Apr 2021 08:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:39:28: #1 finished! INFO @ Sat, 03 Apr 2021 08:39:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:39:28: #2 number of paired peaks: 145 WARNING @ Sat, 03 Apr 2021 08:39:28: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 03 Apr 2021 08:39:28: start model_add_line... INFO @ Sat, 03 Apr 2021 08:39:28: start X-correlation... INFO @ Sat, 03 Apr 2021 08:39:28: end of X-cor INFO @ Sat, 03 Apr 2021 08:39:28: #2 finished! INFO @ Sat, 03 Apr 2021 08:39:28: #2 predicted fragment length is 10 bps INFO @ Sat, 03 Apr 2021 08:39:28: #2 alternative fragment length(s) may be 10,45,79,114,145,155,176,188,225,265,299,335,364,520 bps INFO @ Sat, 03 Apr 2021 08:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.10_model.r WARNING @ Sat, 03 Apr 2021 08:39:28: #2 Since the d (10) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:39:28: #2 You may need to consider one of the other alternative d(s): 10,45,79,114,145,155,176,188,225,265,299,335,364,520 WARNING @ Sat, 03 Apr 2021 08:39:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:39:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:39:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:39:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.10_summits.bed INFO @ Sat, 03 Apr 2021 08:39:28: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:39:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.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, 03 Apr 2021 08:39:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:39:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:39:58: #1 tag size is determined as 54 bps INFO @ Sat, 03 Apr 2021 08:39:58: #1 tag size = 54 INFO @ Sat, 03 Apr 2021 08:39:58: #1 total tags in treatment: 4850 INFO @ Sat, 03 Apr 2021 08:39:58: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:39:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:39:58: #1 tags after filtering in treatment: 4849 INFO @ Sat, 03 Apr 2021 08:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:39:58: #1 finished! INFO @ Sat, 03 Apr 2021 08:39:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:39:58: #2 number of paired peaks: 145 WARNING @ Sat, 03 Apr 2021 08:39:58: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 03 Apr 2021 08:39:58: start model_add_line... INFO @ Sat, 03 Apr 2021 08:39:58: start X-correlation... INFO @ Sat, 03 Apr 2021 08:39:58: end of X-cor INFO @ Sat, 03 Apr 2021 08:39:58: #2 finished! INFO @ Sat, 03 Apr 2021 08:39:58: #2 predicted fragment length is 10 bps INFO @ Sat, 03 Apr 2021 08:39:58: #2 alternative fragment length(s) may be 10,45,79,114,145,155,176,188,225,265,299,335,364,520 bps INFO @ Sat, 03 Apr 2021 08:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.20_model.r WARNING @ Sat, 03 Apr 2021 08:39:58: #2 Since the d (10) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:39:58: #2 You may need to consider one of the other alternative d(s): 10,45,79,114,145,155,176,188,225,265,299,335,364,520 WARNING @ Sat, 03 Apr 2021 08:39:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:39:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:39:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7282591/SRX7282591.20_summits.bed INFO @ Sat, 03 Apr 2021 08:39:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling