Job ID = 12266686 SRX = SRX8622121 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13002672 spots for SRR12096681/SRR12096681.sra Written 13002672 spots for SRR12096681/SRR12096681.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267113 ("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: 00:31:03 13002672 reads; of these: 13002672 (100.00%) were paired; of these: 9013779 (69.32%) aligned concordantly 0 times 3113781 (23.95%) aligned concordantly exactly 1 time 875112 (6.73%) aligned concordantly >1 times ---- 9013779 pairs aligned concordantly 0 times; of these: 881141 (9.78%) aligned discordantly 1 time ---- 8132638 pairs aligned 0 times concordantly or discordantly; of these: 16265276 mates make up the pairs; of these: 15225645 (93.61%) aligned 0 times 362941 (2.23%) aligned exactly 1 time 676690 (4.16%) aligned >1 times 41.45% overall alignment rate Time searching: 00:31:03 Overall time: 00:31:03 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_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] 443578 / 4839304 = 0.0917 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 09:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.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 09:45:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:45:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:45:27: 1000000 INFO @ Sat, 03 Apr 2021 09:45:36: 2000000 INFO @ Sat, 03 Apr 2021 09:45:46: 3000000 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 09:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.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 09:45:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:45:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:45:55: 4000000 INFO @ Sat, 03 Apr 2021 09:45:57: 1000000 INFO @ Sat, 03 Apr 2021 09:46:04: 5000000 INFO @ Sat, 03 Apr 2021 09:46:06: 2000000 INFO @ Sat, 03 Apr 2021 09:46:14: 6000000 INFO @ Sat, 03 Apr 2021 09:46:15: 3000000 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 INFO @ Sat, 03 Apr 2021 09:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.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 09:46:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:46:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:46:24: 7000000 INFO @ Sat, 03 Apr 2021 09:46:25: 4000000 INFO @ Sat, 03 Apr 2021 09:46:29: 1000000 INFO @ Sat, 03 Apr 2021 09:46:34: 5000000 INFO @ Sat, 03 Apr 2021 09:46:35: 8000000 INFO @ Sat, 03 Apr 2021 09:46:40: 2000000 INFO @ Sat, 03 Apr 2021 09:46:43: 6000000 INFO @ Sat, 03 Apr 2021 09:46:46: 9000000 INFO @ Sat, 03 Apr 2021 09:46:51: 3000000 INFO @ Sat, 03 Apr 2021 09:46:52: 7000000 INFO @ Sat, 03 Apr 2021 09:46:55: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:46:55: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:46:55: #1 total tags in treatment: 3596782 INFO @ Sat, 03 Apr 2021 09:46:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:46:55: #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 09:46:55: #1 tags after filtering in treatment: 3295023 INFO @ Sat, 03 Apr 2021 09:46:55: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 03 Apr 2021 09:46:55: #1 finished! INFO @ Sat, 03 Apr 2021 09:46:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:46:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:46:56: #2 number of paired peaks: 702 WARNING @ Sat, 03 Apr 2021 09:46:56: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sat, 03 Apr 2021 09:46:56: start model_add_line... INFO @ Sat, 03 Apr 2021 09:46:56: start X-correlation... INFO @ Sat, 03 Apr 2021 09:46:56: end of X-cor INFO @ Sat, 03 Apr 2021 09:46:56: #2 finished! INFO @ Sat, 03 Apr 2021 09:46:56: #2 predicted fragment length is 195 bps INFO @ Sat, 03 Apr 2021 09:46:56: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 03 Apr 2021 09:46:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.05_model.r WARNING @ Sat, 03 Apr 2021 09:46:56: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:46:56: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 03 Apr 2021 09:46:56: #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 09:46:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:47:00: 4000000 INFO @ Sat, 03 Apr 2021 09:47:01: 8000000 INFO @ Sat, 03 Apr 2021 09:47:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:47:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:47:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:47:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.05_summits.bed INFO @ Sat, 03 Apr 2021 09:47:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1752 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:47:09: 5000000 INFO @ Sat, 03 Apr 2021 09:47:10: 9000000 INFO @ Sat, 03 Apr 2021 09:47:18: 6000000 INFO @ Sat, 03 Apr 2021 09:47:18: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:47:18: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:47:18: #1 total tags in treatment: 3596782 INFO @ Sat, 03 Apr 2021 09:47:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:47:18: #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 09:47:18: #1 tags after filtering in treatment: 3295023 INFO @ Sat, 03 Apr 2021 09:47:18: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 03 Apr 2021 09:47:18: #1 finished! INFO @ Sat, 03 Apr 2021 09:47:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:47:18: #2 number of paired peaks: 702 WARNING @ Sat, 03 Apr 2021 09:47:18: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sat, 03 Apr 2021 09:47:18: start model_add_line... INFO @ Sat, 03 Apr 2021 09:47:18: start X-correlation... INFO @ Sat, 03 Apr 2021 09:47:18: end of X-cor INFO @ Sat, 03 Apr 2021 09:47:18: #2 finished! INFO @ Sat, 03 Apr 2021 09:47:18: #2 predicted fragment length is 195 bps INFO @ Sat, 03 Apr 2021 09:47:18: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 03 Apr 2021 09:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.10_model.r WARNING @ Sat, 03 Apr 2021 09:47:18: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:47:18: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 03 Apr 2021 09:47:18: #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 09:47:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:47:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:47:25: 7000000 INFO @ Sat, 03 Apr 2021 09:47:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:47:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:47:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.10_summits.bed INFO @ Sat, 03 Apr 2021 09:47:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:47:33: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:47:41: 9000000 INFO @ Sat, 03 Apr 2021 09:47:49: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:47:49: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:47:49: #1 total tags in treatment: 3596782 INFO @ Sat, 03 Apr 2021 09:47:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:47:49: #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 09:47:49: #1 tags after filtering in treatment: 3295023 INFO @ Sat, 03 Apr 2021 09:47:49: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 03 Apr 2021 09:47:49: #1 finished! INFO @ Sat, 03 Apr 2021 09:47:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:47:50: #2 number of paired peaks: 702 WARNING @ Sat, 03 Apr 2021 09:47:50: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sat, 03 Apr 2021 09:47:50: start model_add_line... INFO @ Sat, 03 Apr 2021 09:47:50: start X-correlation... INFO @ Sat, 03 Apr 2021 09:47:50: end of X-cor INFO @ Sat, 03 Apr 2021 09:47:50: #2 finished! INFO @ Sat, 03 Apr 2021 09:47:50: #2 predicted fragment length is 195 bps INFO @ Sat, 03 Apr 2021 09:47:50: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 03 Apr 2021 09:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.20_model.r WARNING @ Sat, 03 Apr 2021 09:47:50: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:47:50: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 03 Apr 2021 09:47:50: #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 09:47:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:47:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622121/SRX8622121.20_summits.bed INFO @ Sat, 03 Apr 2021 09:48:00: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。