Job ID = 14166976 SRX = SRX7541134 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17334301 spots for SRR10871136/SRR10871136.sra Written 17334301 spots for SRR10871136/SRR10871136.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167350 ("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: 00:23:46 17334301 reads; of these: 17334301 (100.00%) were paired; of these: 10819091 (62.41%) aligned concordantly 0 times 5098815 (29.41%) aligned concordantly exactly 1 time 1416395 (8.17%) aligned concordantly >1 times ---- 10819091 pairs aligned concordantly 0 times; of these: 508958 (4.70%) aligned discordantly 1 time ---- 10310133 pairs aligned 0 times concordantly or discordantly; of these: 20620266 mates make up the pairs; of these: 19006213 (92.17%) aligned 0 times 676535 (3.28%) aligned exactly 1 time 937518 (4.55%) aligned >1 times 45.18% overall alignment rate Time searching: 00:23:46 Overall time: 00:23:46 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] 1942577 / 7015210 = 0.2769 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 08:48:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.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 08:48:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:48:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:49:01: 1000000 INFO @ Fri, 10 Dec 2021 08:49:08: 2000000 INFO @ Fri, 10 Dec 2021 08:49:16: 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 08:49:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.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 08:49:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:49:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:49:24: 4000000 INFO @ Fri, 10 Dec 2021 08:49:31: 1000000 INFO @ Fri, 10 Dec 2021 08:49:32: 5000000 INFO @ Fri, 10 Dec 2021 08:49:39: 2000000 INFO @ Fri, 10 Dec 2021 08:49:40: 6000000 INFO @ Fri, 10 Dec 2021 08:49:47: 3000000 INFO @ Fri, 10 Dec 2021 08:49:49: 7000000 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 08:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.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 08:49:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:49:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:49:56: 4000000 INFO @ Fri, 10 Dec 2021 08:49:57: 8000000 INFO @ Fri, 10 Dec 2021 08:50:01: 1000000 INFO @ Fri, 10 Dec 2021 08:50:04: 5000000 INFO @ Fri, 10 Dec 2021 08:50:06: 9000000 INFO @ Fri, 10 Dec 2021 08:50:10: 2000000 INFO @ Fri, 10 Dec 2021 08:50:12: 6000000 INFO @ Fri, 10 Dec 2021 08:50:14: 10000000 INFO @ Fri, 10 Dec 2021 08:50:18: 3000000 INFO @ Fri, 10 Dec 2021 08:50:21: 7000000 INFO @ Fri, 10 Dec 2021 08:50:23: 11000000 INFO @ Fri, 10 Dec 2021 08:50:27: 4000000 INFO @ Fri, 10 Dec 2021 08:50:29: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:50:29: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:50:29: #1 total tags in treatment: 4637365 INFO @ Fri, 10 Dec 2021 08:50:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:50:29: #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 08:50:29: 8000000 INFO @ Fri, 10 Dec 2021 08:50:29: #1 tags after filtering in treatment: 4419467 INFO @ Fri, 10 Dec 2021 08:50:29: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 08:50:29: #1 finished! INFO @ Fri, 10 Dec 2021 08:50:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:50:30: #2 number of paired peaks: 501 WARNING @ Fri, 10 Dec 2021 08:50:30: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Fri, 10 Dec 2021 08:50:30: start model_add_line... INFO @ Fri, 10 Dec 2021 08:50:30: start X-correlation... INFO @ Fri, 10 Dec 2021 08:50:30: end of X-cor INFO @ Fri, 10 Dec 2021 08:50:30: #2 finished! INFO @ Fri, 10 Dec 2021 08:50:30: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 08:50:30: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 08:50:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.05_model.r WARNING @ Fri, 10 Dec 2021 08:50:30: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:50:30: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Fri, 10 Dec 2021 08:50:30: #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 08:50:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:50:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:50:35: 5000000 INFO @ Fri, 10 Dec 2021 08:50:37: 9000000 INFO @ Fri, 10 Dec 2021 08:50:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:50:43: 6000000 INFO @ Fri, 10 Dec 2021 08:50:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:50:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:50:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.05_summits.bed INFO @ Fri, 10 Dec 2021 08:50:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3022 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:50:46: 10000000 INFO @ Fri, 10 Dec 2021 08:50:52: 7000000 INFO @ Fri, 10 Dec 2021 08:50:54: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:51:00: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:51:00: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:51:00: #1 total tags in treatment: 4637365 INFO @ Fri, 10 Dec 2021 08:51:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:51:00: #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 08:51:00: #1 tags after filtering in treatment: 4419467 INFO @ Fri, 10 Dec 2021 08:51:00: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 08:51:00: #1 finished! INFO @ Fri, 10 Dec 2021 08:51:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:51:01: #2 number of paired peaks: 501 WARNING @ Fri, 10 Dec 2021 08:51:01: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Fri, 10 Dec 2021 08:51:01: start model_add_line... INFO @ Fri, 10 Dec 2021 08:51:01: 8000000 INFO @ Fri, 10 Dec 2021 08:51:01: start X-correlation... INFO @ Fri, 10 Dec 2021 08:51:01: end of X-cor INFO @ Fri, 10 Dec 2021 08:51:01: #2 finished! INFO @ Fri, 10 Dec 2021 08:51:01: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 08:51:01: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 08:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.10_model.r WARNING @ Fri, 10 Dec 2021 08:51:01: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:51:01: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Fri, 10 Dec 2021 08:51:01: #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 08:51:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:51:09: 9000000 INFO @ Fri, 10 Dec 2021 08:51:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.10_summits.bed INFO @ Fri, 10 Dec 2021 08:51:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1192 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:51:17: 10000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:51:25: 11000000 INFO @ Fri, 10 Dec 2021 08:51:31: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:51:31: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:51:31: #1 total tags in treatment: 4637365 INFO @ Fri, 10 Dec 2021 08:51:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:51:31: #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 08:51:31: #1 tags after filtering in treatment: 4419467 INFO @ Fri, 10 Dec 2021 08:51:31: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 10 Dec 2021 08:51:31: #1 finished! INFO @ Fri, 10 Dec 2021 08:51:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:51:31: #2 number of paired peaks: 501 WARNING @ Fri, 10 Dec 2021 08:51:31: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Fri, 10 Dec 2021 08:51:31: start model_add_line... INFO @ Fri, 10 Dec 2021 08:51:31: start X-correlation... INFO @ Fri, 10 Dec 2021 08:51:31: end of X-cor INFO @ Fri, 10 Dec 2021 08:51:31: #2 finished! INFO @ Fri, 10 Dec 2021 08:51:31: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Dec 2021 08:51:31: #2 alternative fragment length(s) may be 158 bps INFO @ Fri, 10 Dec 2021 08:51:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.20_model.r WARNING @ Fri, 10 Dec 2021 08:51:31: #2 Since the d (158) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:51:31: #2 You may need to consider one of the other alternative d(s): 158 WARNING @ Fri, 10 Dec 2021 08:51:31: #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 08:51:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:51:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:51:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541134/SRX7541134.20_summits.bed INFO @ Fri, 10 Dec 2021 08:51:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 1 millis CompletedMACS2peakCalling