Job ID = 14170591 SRX = SRX8497049 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10822128 spots for SRR11952648/SRR11952648.sra Written 10822128 spots for SRR11952648/SRR11952648.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171033 ("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: 00:16:14 10822128 reads; of these: 10822128 (100.00%) were paired; of these: 5345732 (49.40%) aligned concordantly 0 times 3579674 (33.08%) aligned concordantly exactly 1 time 1896722 (17.53%) aligned concordantly >1 times ---- 5345732 pairs aligned concordantly 0 times; of these: 172868 (3.23%) aligned discordantly 1 time ---- 5172864 pairs aligned 0 times concordantly or discordantly; of these: 10345728 mates make up the pairs; of these: 9982842 (96.49%) aligned 0 times 158270 (1.53%) aligned exactly 1 time 204616 (1.98%) aligned >1 times 53.88% overall alignment rate Time searching: 00:16:14 Overall time: 00:16:14 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2025308 / 5637934 = 0.3592 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 07:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.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 07:43:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:43:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:43:26: 1000000 INFO @ Sat, 11 Dec 2021 07:43:32: 2000000 INFO @ Sat, 11 Dec 2021 07:43:39: 3000000 INFO @ Sat, 11 Dec 2021 07:43:45: 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 07:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.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 07:43:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:43:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:43:53: 5000000 INFO @ Sat, 11 Dec 2021 07:43:57: 1000000 INFO @ Sat, 11 Dec 2021 07:44:01: 6000000 INFO @ Sat, 11 Dec 2021 07:44:05: 2000000 INFO @ Sat, 11 Dec 2021 07:44:09: 7000000 INFO @ Sat, 11 Dec 2021 07:44:14: 3000000 INFO @ Sat, 11 Dec 2021 07:44:14: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:44:14: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:44:14: #1 total tags in treatment: 3498676 INFO @ Sat, 11 Dec 2021 07:44:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:44:14: #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 07:44:14: #1 tags after filtering in treatment: 3214931 INFO @ Sat, 11 Dec 2021 07:44:14: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 07:44:14: #1 finished! INFO @ Sat, 11 Dec 2021 07:44:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:44:14: #2 number of paired peaks: 561 WARNING @ Sat, 11 Dec 2021 07:44:14: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 11 Dec 2021 07:44:14: start model_add_line... INFO @ Sat, 11 Dec 2021 07:44:14: start X-correlation... INFO @ Sat, 11 Dec 2021 07:44:14: end of X-cor INFO @ Sat, 11 Dec 2021 07:44:14: #2 finished! INFO @ Sat, 11 Dec 2021 07:44:14: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 07:44:14: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 07:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.05_model.r WARNING @ Sat, 11 Dec 2021 07:44:14: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:44:14: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sat, 11 Dec 2021 07:44:14: #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 07:44:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:44:14: #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 @ Sat, 11 Dec 2021 07:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.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 07:44:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:44:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:44:21: 4000000 INFO @ Sat, 11 Dec 2021 07:44:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:44:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:44:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.05_summits.bed INFO @ Sat, 11 Dec 2021 07:44:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1505 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:44:27: 1000000 INFO @ Sat, 11 Dec 2021 07:44:29: 5000000 INFO @ Sat, 11 Dec 2021 07:44:35: 2000000 INFO @ Sat, 11 Dec 2021 07:44:37: 6000000 INFO @ Sat, 11 Dec 2021 07:44:44: 3000000 INFO @ Sat, 11 Dec 2021 07:44:46: 7000000 INFO @ Sat, 11 Dec 2021 07:44:50: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:44:50: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:44:50: #1 total tags in treatment: 3498676 INFO @ Sat, 11 Dec 2021 07:44:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:44:50: #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 07:44:50: #1 tags after filtering in treatment: 3214931 INFO @ Sat, 11 Dec 2021 07:44:50: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 07:44:50: #1 finished! INFO @ Sat, 11 Dec 2021 07:44:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:44:51: #2 number of paired peaks: 561 WARNING @ Sat, 11 Dec 2021 07:44:51: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 11 Dec 2021 07:44:51: start model_add_line... INFO @ Sat, 11 Dec 2021 07:44:51: start X-correlation... INFO @ Sat, 11 Dec 2021 07:44:51: end of X-cor INFO @ Sat, 11 Dec 2021 07:44:51: #2 finished! INFO @ Sat, 11 Dec 2021 07:44:51: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 07:44:51: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 07:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.10_model.r WARNING @ Sat, 11 Dec 2021 07:44:51: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:44:51: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sat, 11 Dec 2021 07:44:51: #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 07:44:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:44:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:44:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:44:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:44:59: 5000000 INFO @ Sat, 11 Dec 2021 07:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.10_summits.bed INFO @ Sat, 11 Dec 2021 07:45:01: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (733 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:45:07: 6000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:45:14: 7000000 INFO @ Sat, 11 Dec 2021 07:45:19: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 07:45:19: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 07:45:19: #1 total tags in treatment: 3498676 INFO @ Sat, 11 Dec 2021 07:45:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:45:19: #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 07:45:19: #1 tags after filtering in treatment: 3214931 INFO @ Sat, 11 Dec 2021 07:45:19: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 11 Dec 2021 07:45:19: #1 finished! INFO @ Sat, 11 Dec 2021 07:45:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:45:19: #2 number of paired peaks: 561 WARNING @ Sat, 11 Dec 2021 07:45:19: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Sat, 11 Dec 2021 07:45:19: start model_add_line... INFO @ Sat, 11 Dec 2021 07:45:19: start X-correlation... INFO @ Sat, 11 Dec 2021 07:45:19: end of X-cor INFO @ Sat, 11 Dec 2021 07:45:19: #2 finished! INFO @ Sat, 11 Dec 2021 07:45:19: #2 predicted fragment length is 165 bps INFO @ Sat, 11 Dec 2021 07:45:19: #2 alternative fragment length(s) may be 165 bps INFO @ Sat, 11 Dec 2021 07:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.20_model.r WARNING @ Sat, 11 Dec 2021 07:45:19: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:45:19: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Sat, 11 Dec 2021 07:45:19: #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 07:45:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:45:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497049/SRX8497049.20_summits.bed INFO @ Sat, 11 Dec 2021 07:45:29: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (344 records, 4 fields): 2 millis CompletedMACS2peakCalling