Job ID = 12265183 SRX = SRX3282116 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34457240 spots for SRR6171267/SRR6171267.sra Written 34457240 spots for SRR6171267/SRR6171267.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265616 ("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: 00:36:08 34457240 reads; of these: 34457240 (100.00%) were paired; of these: 27838814 (80.79%) aligned concordantly 0 times 3325014 (9.65%) aligned concordantly exactly 1 time 3293412 (9.56%) aligned concordantly >1 times ---- 27838814 pairs aligned concordantly 0 times; of these: 761804 (2.74%) aligned discordantly 1 time ---- 27077010 pairs aligned 0 times concordantly or discordantly; of these: 54154020 mates make up the pairs; of these: 52900186 (97.68%) aligned 0 times 267035 (0.49%) aligned exactly 1 time 986799 (1.82%) aligned >1 times 23.24% overall alignment rate Time searching: 00:36:08 Overall time: 00:36:08 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] 1973490 / 7325289 = 0.2694 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 07:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.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 07:28:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:28:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:20: 1000000 INFO @ Sat, 03 Apr 2021 07:28:31: 2000000 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 07:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.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 07:28:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:28:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:28:42: 3000000 INFO @ Sat, 03 Apr 2021 07:28:47: 1000000 INFO @ Sat, 03 Apr 2021 07:28:53: 4000000 INFO @ Sat, 03 Apr 2021 07:28:57: 2000000 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 07:29:05: 5000000 INFO @ Sat, 03 Apr 2021 07:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.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 07:29:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:29:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:29:07: 3000000 INFO @ Sat, 03 Apr 2021 07:29:17: 6000000 INFO @ Sat, 03 Apr 2021 07:29:17: 4000000 INFO @ Sat, 03 Apr 2021 07:29:20: 1000000 INFO @ Sat, 03 Apr 2021 07:29:27: 5000000 INFO @ Sat, 03 Apr 2021 07:29:29: 7000000 INFO @ Sat, 03 Apr 2021 07:29:36: 2000000 INFO @ Sat, 03 Apr 2021 07:29:37: 6000000 INFO @ Sat, 03 Apr 2021 07:29:40: 8000000 INFO @ Sat, 03 Apr 2021 07:29:47: 7000000 INFO @ Sat, 03 Apr 2021 07:29:52: 9000000 INFO @ Sat, 03 Apr 2021 07:29:52: 3000000 INFO @ Sat, 03 Apr 2021 07:29:57: 8000000 INFO @ Sat, 03 Apr 2021 07:30:03: 10000000 INFO @ Sat, 03 Apr 2021 07:30:07: 9000000 INFO @ Sat, 03 Apr 2021 07:30:08: 4000000 INFO @ Sat, 03 Apr 2021 07:30:15: 11000000 INFO @ Sat, 03 Apr 2021 07:30:17: 10000000 INFO @ Sat, 03 Apr 2021 07:30:24: 5000000 INFO @ Sat, 03 Apr 2021 07:30:27: 11000000 INFO @ Sat, 03 Apr 2021 07:30:28: 12000000 INFO @ Sat, 03 Apr 2021 07:30:28: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 07:30:28: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 07:30:28: #1 total tags in treatment: 4699280 INFO @ Sat, 03 Apr 2021 07:30:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:30:28: #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 07:30:28: #1 tags after filtering in treatment: 3703472 INFO @ Sat, 03 Apr 2021 07:30:28: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 07:30:28: #1 finished! INFO @ Sat, 03 Apr 2021 07:30:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:30:29: #2 number of paired peaks: 1469 INFO @ Sat, 03 Apr 2021 07:30:29: start model_add_line... INFO @ Sat, 03 Apr 2021 07:30:29: start X-correlation... INFO @ Sat, 03 Apr 2021 07:30:29: end of X-cor INFO @ Sat, 03 Apr 2021 07:30:29: #2 finished! INFO @ Sat, 03 Apr 2021 07:30:29: #2 predicted fragment length is 149 bps INFO @ Sat, 03 Apr 2021 07:30:29: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 03 Apr 2021 07:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.05_model.r WARNING @ Sat, 03 Apr 2021 07:30:29: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:30:29: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 03 Apr 2021 07:30:29: #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 07:30:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:30:38: 12000000 INFO @ Sat, 03 Apr 2021 07:30:38: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 07:30:38: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 07:30:38: #1 total tags in treatment: 4699280 INFO @ Sat, 03 Apr 2021 07:30:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:30:38: #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 07:30:38: #1 tags after filtering in treatment: 3703472 INFO @ Sat, 03 Apr 2021 07:30:38: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 07:30:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:30:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:30:39: #2 number of paired peaks: 1469 INFO @ Sat, 03 Apr 2021 07:30:39: start model_add_line... INFO @ Sat, 03 Apr 2021 07:30:39: start X-correlation... INFO @ Sat, 03 Apr 2021 07:30:39: end of X-cor INFO @ Sat, 03 Apr 2021 07:30:39: #2 finished! INFO @ Sat, 03 Apr 2021 07:30:39: #2 predicted fragment length is 149 bps INFO @ Sat, 03 Apr 2021 07:30:39: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 03 Apr 2021 07:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.10_model.r WARNING @ Sat, 03 Apr 2021 07:30:39: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:30:39: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 03 Apr 2021 07:30:39: #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 07:30:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:30:40: 6000000 INFO @ Sat, 03 Apr 2021 07:30:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.05_summits.bed INFO @ Sat, 03 Apr 2021 07:30:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3715 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:30:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:30:54: 7000000 INFO @ Sat, 03 Apr 2021 07:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.10_summits.bed INFO @ Sat, 03 Apr 2021 07:30:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1691 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:31:08: 8000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:31:22: 9000000 INFO @ Sat, 03 Apr 2021 07:31:37: 10000000 INFO @ Sat, 03 Apr 2021 07:31:51: 11000000 INFO @ Sat, 03 Apr 2021 07:32:05: 12000000 INFO @ Sat, 03 Apr 2021 07:32:06: #1 tag size is determined as 100 bps INFO @ Sat, 03 Apr 2021 07:32:06: #1 tag size = 100 INFO @ Sat, 03 Apr 2021 07:32:06: #1 total tags in treatment: 4699280 INFO @ Sat, 03 Apr 2021 07:32:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:32:06: #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 07:32:06: #1 tags after filtering in treatment: 3703472 INFO @ Sat, 03 Apr 2021 07:32:06: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 07:32:06: #1 finished! INFO @ Sat, 03 Apr 2021 07:32:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:32:06: #2 number of paired peaks: 1469 INFO @ Sat, 03 Apr 2021 07:32:06: start model_add_line... INFO @ Sat, 03 Apr 2021 07:32:06: start X-correlation... INFO @ Sat, 03 Apr 2021 07:32:06: end of X-cor INFO @ Sat, 03 Apr 2021 07:32:06: #2 finished! INFO @ Sat, 03 Apr 2021 07:32:06: #2 predicted fragment length is 149 bps INFO @ Sat, 03 Apr 2021 07:32:06: #2 alternative fragment length(s) may be 149 bps INFO @ Sat, 03 Apr 2021 07:32:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.20_model.r WARNING @ Sat, 03 Apr 2021 07:32:06: #2 Since the d (149) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:32:06: #2 You may need to consider one of the other alternative d(s): 149 WARNING @ Sat, 03 Apr 2021 07:32:06: #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 07:32:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:32:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:32:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3282116/SRX3282116.20_summits.bed INFO @ Sat, 03 Apr 2021 07:32:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (573 records, 4 fields): 3 millis CompletedMACS2peakCalling