Job ID = 12266670 SRX = SRX7806737 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18679753 spots for SRR11186403/SRR11186403.sra Written 18679753 spots for SRR11186403/SRR11186403.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266974 ("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: 00:20:59 18679753 reads; of these: 18679753 (100.00%) were paired; of these: 11458388 (61.34%) aligned concordantly 0 times 4532267 (24.26%) aligned concordantly exactly 1 time 2689098 (14.40%) aligned concordantly >1 times ---- 11458388 pairs aligned concordantly 0 times; of these: 1019819 (8.90%) aligned discordantly 1 time ---- 10438569 pairs aligned 0 times concordantly or discordantly; of these: 20877138 mates make up the pairs; of these: 19405213 (92.95%) aligned 0 times 575263 (2.76%) aligned exactly 1 time 896662 (4.29%) aligned >1 times 48.06% overall alignment rate Time searching: 00:20:59 Overall time: 00:20:59 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] 2086249 / 8188773 = 0.2548 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 09:32:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.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 09:32:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:32:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:32:56: 1000000 INFO @ Sat, 03 Apr 2021 09:33:04: 2000000 INFO @ Sat, 03 Apr 2021 09:33:11: 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 09:33:18: 4000000 INFO @ Sat, 03 Apr 2021 09:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.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 09:33:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:33:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:33:26: 5000000 INFO @ Sat, 03 Apr 2021 09:33:28: 1000000 INFO @ Sat, 03 Apr 2021 09:33:35: 6000000 INFO @ Sat, 03 Apr 2021 09:33:37: 2000000 INFO @ Sat, 03 Apr 2021 09:33:44: 7000000 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 09:33:47: 3000000 INFO @ Sat, 03 Apr 2021 09:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.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 09:33:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:33:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:33:53: 8000000 INFO @ Sat, 03 Apr 2021 09:33:57: 4000000 INFO @ Sat, 03 Apr 2021 09:33:59: 1000000 INFO @ Sat, 03 Apr 2021 09:34:02: 9000000 INFO @ Sat, 03 Apr 2021 09:34:08: 5000000 INFO @ Sat, 03 Apr 2021 09:34:09: 2000000 INFO @ Sat, 03 Apr 2021 09:34:10: 10000000 INFO @ Sat, 03 Apr 2021 09:34:18: 6000000 INFO @ Sat, 03 Apr 2021 09:34:18: 3000000 INFO @ Sat, 03 Apr 2021 09:34:19: 11000000 INFO @ Sat, 03 Apr 2021 09:34:27: 4000000 INFO @ Sat, 03 Apr 2021 09:34:28: 7000000 INFO @ Sat, 03 Apr 2021 09:34:28: 12000000 INFO @ Sat, 03 Apr 2021 09:34:36: 5000000 INFO @ Sat, 03 Apr 2021 09:34:37: 13000000 INFO @ Sat, 03 Apr 2021 09:34:38: 8000000 INFO @ Sat, 03 Apr 2021 09:34:44: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:34:44: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:34:44: #1 total tags in treatment: 5267186 INFO @ Sat, 03 Apr 2021 09:34:44: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:34:44: #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 09:34:44: #1 tags after filtering in treatment: 4252551 INFO @ Sat, 03 Apr 2021 09:34:44: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:34:44: #1 finished! INFO @ Sat, 03 Apr 2021 09:34:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:34:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:34:45: #2 number of paired peaks: 1232 INFO @ Sat, 03 Apr 2021 09:34:45: start model_add_line... INFO @ Sat, 03 Apr 2021 09:34:45: start X-correlation... INFO @ Sat, 03 Apr 2021 09:34:45: end of X-cor INFO @ Sat, 03 Apr 2021 09:34:45: #2 finished! INFO @ Sat, 03 Apr 2021 09:34:45: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Apr 2021 09:34:45: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 03 Apr 2021 09:34:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.05_model.r WARNING @ Sat, 03 Apr 2021 09:34:45: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:34:45: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 03 Apr 2021 09:34:45: #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 09:34:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:34:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:34:45: 6000000 INFO @ Sat, 03 Apr 2021 09:34:48: 9000000 INFO @ Sat, 03 Apr 2021 09:34:54: 7000000 INFO @ Sat, 03 Apr 2021 09:34:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:34:58: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:35:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:35:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:35:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.05_summits.bed INFO @ Sat, 03 Apr 2021 09:35:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5282 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:35:03: 8000000 INFO @ Sat, 03 Apr 2021 09:35:08: 11000000 INFO @ Sat, 03 Apr 2021 09:35:12: 9000000 INFO @ Sat, 03 Apr 2021 09:35:18: 12000000 INFO @ Sat, 03 Apr 2021 09:35:21: 10000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:35:28: 13000000 INFO @ Sat, 03 Apr 2021 09:35:30: 11000000 INFO @ Sat, 03 Apr 2021 09:35:36: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:35:36: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:35:36: #1 total tags in treatment: 5267186 INFO @ Sat, 03 Apr 2021 09:35:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:35:36: #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 09:35:36: #1 tags after filtering in treatment: 4252551 INFO @ Sat, 03 Apr 2021 09:35:36: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:35:36: #1 finished! INFO @ Sat, 03 Apr 2021 09:35:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:35:36: #2 number of paired peaks: 1232 INFO @ Sat, 03 Apr 2021 09:35:36: start model_add_line... INFO @ Sat, 03 Apr 2021 09:35:36: start X-correlation... INFO @ Sat, 03 Apr 2021 09:35:36: end of X-cor INFO @ Sat, 03 Apr 2021 09:35:36: #2 finished! INFO @ Sat, 03 Apr 2021 09:35:36: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Apr 2021 09:35:36: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 03 Apr 2021 09:35:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.10_model.r WARNING @ Sat, 03 Apr 2021 09:35:36: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:35:36: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 03 Apr 2021 09:35:36: #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 09:35:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:35:38: 12000000 INFO @ Sat, 03 Apr 2021 09:35:46: 13000000 INFO @ Sat, 03 Apr 2021 09:35:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:35:51: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:35:51: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:35:51: #1 total tags in treatment: 5267186 INFO @ Sat, 03 Apr 2021 09:35:51: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:35:51: #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 09:35:51: #1 tags after filtering in treatment: 4252551 INFO @ Sat, 03 Apr 2021 09:35:51: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:35:51: #1 finished! INFO @ Sat, 03 Apr 2021 09:35:51: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:35:52: #2 number of paired peaks: 1232 INFO @ Sat, 03 Apr 2021 09:35:52: start model_add_line... INFO @ Sat, 03 Apr 2021 09:35:52: start X-correlation... INFO @ Sat, 03 Apr 2021 09:35:52: end of X-cor INFO @ Sat, 03 Apr 2021 09:35:52: #2 finished! INFO @ Sat, 03 Apr 2021 09:35:52: #2 predicted fragment length is 139 bps INFO @ Sat, 03 Apr 2021 09:35:52: #2 alternative fragment length(s) may be 139 bps INFO @ Sat, 03 Apr 2021 09:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.20_model.r WARNING @ Sat, 03 Apr 2021 09:35:52: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:35:52: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Sat, 03 Apr 2021 09:35:52: #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 09:35:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.10_summits.bed INFO @ Sat, 03 Apr 2021 09:35:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1921 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:36:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:36:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806737/SRX7806737.20_summits.bed INFO @ Sat, 03 Apr 2021 09:36:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 2 millis CompletedMACS2peakCalling