Job ID = 14166948 SRX = SRX7541109 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17416551 spots for SRR10871161/SRR10871161.sra Written 17416551 spots for SRR10871161/SRR10871161.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167356 ("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: 00:42:24 17416551 reads; of these: 17416551 (100.00%) were paired; of these: 9871157 (56.68%) aligned concordantly 0 times 5488336 (31.51%) aligned concordantly exactly 1 time 2057058 (11.81%) aligned concordantly >1 times ---- 9871157 pairs aligned concordantly 0 times; of these: 663569 (6.72%) aligned discordantly 1 time ---- 9207588 pairs aligned 0 times concordantly or discordantly; of these: 18415176 mates make up the pairs; of these: 17000953 (92.32%) aligned 0 times 510163 (2.77%) aligned exactly 1 time 904060 (4.91%) aligned >1 times 51.19% overall alignment rate Time searching: 00:42:24 Overall time: 00:42:24 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] 4185400 / 8193834 = 0.5108 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 08:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.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 08:56:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:56:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:56:51: 1000000 INFO @ Fri, 10 Dec 2021 08:57:00: 2000000 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 08:57:09: 3000000 INFO @ Fri, 10 Dec 2021 08:57:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.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 08:57:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:57:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:57:18: 4000000 INFO @ Fri, 10 Dec 2021 08:57:20: 1000000 INFO @ Fri, 10 Dec 2021 08:57:27: 5000000 INFO @ Fri, 10 Dec 2021 08:57:29: 2000000 INFO @ Fri, 10 Dec 2021 08:57:36: 6000000 INFO @ Fri, 10 Dec 2021 08:57:38: 3000000 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 08:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.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 08:57:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:57:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:57:45: 7000000 INFO @ Fri, 10 Dec 2021 08:57:47: 4000000 INFO @ Fri, 10 Dec 2021 08:57:49: 1000000 INFO @ Fri, 10 Dec 2021 08:57:55: 8000000 INFO @ Fri, 10 Dec 2021 08:57:56: 5000000 INFO @ Fri, 10 Dec 2021 08:57:57: 2000000 INFO @ Fri, 10 Dec 2021 08:58:04: 3000000 INFO @ Fri, 10 Dec 2021 08:58:04: 9000000 INFO @ Fri, 10 Dec 2021 08:58:05: 6000000 INFO @ Fri, 10 Dec 2021 08:58:09: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:58:09: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:58:09: #1 total tags in treatment: 3543687 INFO @ Fri, 10 Dec 2021 08:58:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:58:09: #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 08:58:09: #1 tags after filtering in treatment: 3320029 INFO @ Fri, 10 Dec 2021 08:58:09: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 08:58:09: #1 finished! INFO @ Fri, 10 Dec 2021 08:58:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:58:09: #2 number of paired peaks: 1166 INFO @ Fri, 10 Dec 2021 08:58:09: start model_add_line... INFO @ Fri, 10 Dec 2021 08:58:09: start X-correlation... INFO @ Fri, 10 Dec 2021 08:58:09: end of X-cor INFO @ Fri, 10 Dec 2021 08:58:09: #2 finished! INFO @ Fri, 10 Dec 2021 08:58:09: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 08:58:09: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 08:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.05_model.r WARNING @ Fri, 10 Dec 2021 08:58:09: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:58:09: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 08:58:09: #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 08:58:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:58:11: 4000000 INFO @ Fri, 10 Dec 2021 08:58:14: 7000000 INFO @ Fri, 10 Dec 2021 08:58:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:58:19: 5000000 INFO @ Fri, 10 Dec 2021 08:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.05_summits.bed INFO @ Fri, 10 Dec 2021 08:58:21: Done! INFO @ Fri, 10 Dec 2021 08:58:23: 8000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2930 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:58:26: 6000000 INFO @ Fri, 10 Dec 2021 08:58:31: 9000000 INFO @ Fri, 10 Dec 2021 08:58:33: 7000000 INFO @ Fri, 10 Dec 2021 08:58:36: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:58:36: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:58:36: #1 total tags in treatment: 3543687 INFO @ Fri, 10 Dec 2021 08:58:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:58:36: #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 08:58:36: #1 tags after filtering in treatment: 3320029 INFO @ Fri, 10 Dec 2021 08:58:36: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 08:58:36: #1 finished! INFO @ Fri, 10 Dec 2021 08:58:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:58:37: #2 number of paired peaks: 1166 INFO @ Fri, 10 Dec 2021 08:58:37: start model_add_line... INFO @ Fri, 10 Dec 2021 08:58:37: start X-correlation... INFO @ Fri, 10 Dec 2021 08:58:37: end of X-cor INFO @ Fri, 10 Dec 2021 08:58:37: #2 finished! INFO @ Fri, 10 Dec 2021 08:58:37: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 08:58:37: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 08:58:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.10_model.r WARNING @ Fri, 10 Dec 2021 08:58:37: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:58:37: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 08:58:37: #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 08:58:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:58:40: 8000000 INFO @ Fri, 10 Dec 2021 08:58:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:58:47: 9000000 INFO @ Fri, 10 Dec 2021 08:58:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:58:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:58:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.10_summits.bed INFO @ Fri, 10 Dec 2021 08:58:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:58:51: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 08:58:51: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 08:58:51: #1 total tags in treatment: 3543687 INFO @ Fri, 10 Dec 2021 08:58:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:58:51: #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 08:58:51: #1 tags after filtering in treatment: 3320029 INFO @ Fri, 10 Dec 2021 08:58:51: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 08:58:51: #1 finished! INFO @ Fri, 10 Dec 2021 08:58:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:58:52: #2 number of paired peaks: 1166 INFO @ Fri, 10 Dec 2021 08:58:52: start model_add_line... INFO @ Fri, 10 Dec 2021 08:58:52: start X-correlation... INFO @ Fri, 10 Dec 2021 08:58:52: end of X-cor INFO @ Fri, 10 Dec 2021 08:58:52: #2 finished! INFO @ Fri, 10 Dec 2021 08:58:52: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 08:58:52: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 08:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.20_model.r WARNING @ Fri, 10 Dec 2021 08:58:52: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:58:52: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 08:58:52: #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 08:58:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:58:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:58:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7541109/SRX7541109.20_summits.bed INFO @ Fri, 10 Dec 2021 08:59:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。