Job ID = 12265485 SRX = SRX7192200 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10978251 spots for SRR10503247/SRR10503247.sra Written 10978251 spots for SRR10503247/SRR10503247.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265659 ("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: 00:16:37 10978251 reads; of these: 10978251 (100.00%) were paired; of these: 3573432 (32.55%) aligned concordantly 0 times 6126863 (55.81%) aligned concordantly exactly 1 time 1277956 (11.64%) aligned concordantly >1 times ---- 3573432 pairs aligned concordantly 0 times; of these: 901771 (25.24%) aligned discordantly 1 time ---- 2671661 pairs aligned 0 times concordantly or discordantly; of these: 5343322 mates make up the pairs; of these: 3703475 (69.31%) aligned 0 times 1224206 (22.91%) aligned exactly 1 time 415641 (7.78%) aligned >1 times 83.13% overall alignment rate Time searching: 00:16:37 Overall time: 00:16:37 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] 2384548 / 8042593 = 0.2965 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 07:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.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 07:41:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:41:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:41:33: 1000000 INFO @ Sat, 03 Apr 2021 07:41:42: 2000000 INFO @ Sat, 03 Apr 2021 07:41:51: 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 07:41:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.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 07:41:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:41:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:01: 4000000 INFO @ Sat, 03 Apr 2021 07:42:03: 1000000 INFO @ Sat, 03 Apr 2021 07:42:11: 5000000 INFO @ Sat, 03 Apr 2021 07:42:11: 2000000 INFO @ Sat, 03 Apr 2021 07:42:20: 3000000 INFO @ Sat, 03 Apr 2021 07:42:21: 6000000 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 07:42:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.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 07:42:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:29: 4000000 INFO @ Sat, 03 Apr 2021 07:42:30: 7000000 INFO @ Sat, 03 Apr 2021 07:42:33: 1000000 INFO @ Sat, 03 Apr 2021 07:42:38: 5000000 INFO @ Sat, 03 Apr 2021 07:42:40: 8000000 INFO @ Sat, 03 Apr 2021 07:42:42: 2000000 INFO @ Sat, 03 Apr 2021 07:42:47: 6000000 INFO @ Sat, 03 Apr 2021 07:42:50: 9000000 INFO @ Sat, 03 Apr 2021 07:42:51: 3000000 INFO @ Sat, 03 Apr 2021 07:42:56: 7000000 INFO @ Sat, 03 Apr 2021 07:43:00: 10000000 INFO @ Sat, 03 Apr 2021 07:43:01: 4000000 INFO @ Sat, 03 Apr 2021 07:43:05: 8000000 INFO @ Sat, 03 Apr 2021 07:43:10: 5000000 INFO @ Sat, 03 Apr 2021 07:43:10: 11000000 INFO @ Sat, 03 Apr 2021 07:43:14: 9000000 INFO @ Sat, 03 Apr 2021 07:43:19: 6000000 INFO @ Sat, 03 Apr 2021 07:43:20: 12000000 INFO @ Sat, 03 Apr 2021 07:43:23: 10000000 INFO @ Sat, 03 Apr 2021 07:43:28: 7000000 INFO @ Sat, 03 Apr 2021 07:43:30: 13000000 INFO @ Sat, 03 Apr 2021 07:43:32: 11000000 INFO @ Sat, 03 Apr 2021 07:43:34: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:43:34: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:43:34: #1 total tags in treatment: 5113652 INFO @ Sat, 03 Apr 2021 07:43:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:43:34: #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 07:43:35: #1 tags after filtering in treatment: 3856862 INFO @ Sat, 03 Apr 2021 07:43:35: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:43:35: #1 finished! INFO @ Sat, 03 Apr 2021 07:43:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:43:35: #2 number of paired peaks: 5264 INFO @ Sat, 03 Apr 2021 07:43:35: start model_add_line... INFO @ Sat, 03 Apr 2021 07:43:35: start X-correlation... INFO @ Sat, 03 Apr 2021 07:43:35: end of X-cor INFO @ Sat, 03 Apr 2021 07:43:35: #2 finished! INFO @ Sat, 03 Apr 2021 07:43:35: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Apr 2021 07:43:35: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 03 Apr 2021 07:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.05_model.r WARNING @ Sat, 03 Apr 2021 07:43:35: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:43:35: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 03 Apr 2021 07:43:35: #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 07:43:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:43:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:43:37: 8000000 INFO @ Sat, 03 Apr 2021 07:43:41: 12000000 INFO @ Sat, 03 Apr 2021 07:43:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:43:45: 9000000 INFO @ Sat, 03 Apr 2021 07:43:49: 13000000 INFO @ Sat, 03 Apr 2021 07:43:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:43:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:43:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.05_summits.bed INFO @ Sat, 03 Apr 2021 07:43:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8979 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:43:53: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:43:53: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:43:53: #1 total tags in treatment: 5113652 INFO @ Sat, 03 Apr 2021 07:43:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:43:53: #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 07:43:53: #1 tags after filtering in treatment: 3856862 INFO @ Sat, 03 Apr 2021 07:43:53: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:43:53: #1 finished! INFO @ Sat, 03 Apr 2021 07:43:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:43:54: 10000000 INFO @ Sat, 03 Apr 2021 07:43:54: #2 number of paired peaks: 5264 INFO @ Sat, 03 Apr 2021 07:43:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:43:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:43:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:43:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:43:54: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Apr 2021 07:43:54: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 03 Apr 2021 07:43:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.10_model.r WARNING @ Sat, 03 Apr 2021 07:43:54: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:43:54: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 03 Apr 2021 07:43:54: #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 07:43:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:43:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:44:01: 11000000 INFO @ Sat, 03 Apr 2021 07:44:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:44:09: 12000000 INFO @ Sat, 03 Apr 2021 07:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.10_summits.bed INFO @ Sat, 03 Apr 2021 07:44:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5609 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:44:16: 13000000 INFO @ Sat, 03 Apr 2021 07:44:20: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:44:20: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:44:20: #1 total tags in treatment: 5113652 INFO @ Sat, 03 Apr 2021 07:44:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:44:20: #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 07:44:20: #1 tags after filtering in treatment: 3856862 INFO @ Sat, 03 Apr 2021 07:44:20: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 03 Apr 2021 07:44:20: #1 finished! INFO @ Sat, 03 Apr 2021 07:44:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:44:21: #2 number of paired peaks: 5264 INFO @ Sat, 03 Apr 2021 07:44:21: start model_add_line... INFO @ Sat, 03 Apr 2021 07:44:21: start X-correlation... INFO @ Sat, 03 Apr 2021 07:44:21: end of X-cor INFO @ Sat, 03 Apr 2021 07:44:21: #2 finished! INFO @ Sat, 03 Apr 2021 07:44:21: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Apr 2021 07:44:21: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 03 Apr 2021 07:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.20_model.r WARNING @ Sat, 03 Apr 2021 07:44:21: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:44:21: #2 You may need to consider one of the other alternative d(s): 191 WARNING @ Sat, 03 Apr 2021 07:44:21: #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 07:44:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:44:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:44:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:44:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:44:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7192200/SRX7192200.20_summits.bed INFO @ Sat, 03 Apr 2021 07:44:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2465 records, 4 fields): 4 millis CompletedMACS2peakCalling