Job ID = 16439989 SRX = SRX12175826 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24788171 spots for SRR15884965/SRR15884965.sra Written 24788171 spots for SRR15884965/SRR15884965.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440094 ("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: 00:25:10 24788171 reads; of these: 24788171 (100.00%) were paired; of these: 19905815 (80.30%) aligned concordantly 0 times 4201357 (16.95%) aligned concordantly exactly 1 time 680999 (2.75%) aligned concordantly >1 times ---- 19905815 pairs aligned concordantly 0 times; of these: 1219563 (6.13%) aligned discordantly 1 time ---- 18686252 pairs aligned 0 times concordantly or discordantly; of these: 37372504 mates make up the pairs; of these: 36671713 (98.12%) aligned 0 times 265068 (0.71%) aligned exactly 1 time 435723 (1.17%) aligned >1 times 26.03% overall alignment rate Time searching: 00:25:10 Overall time: 00:25:10 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 12 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] 798623 / 6060254 = 0.1318 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.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 @ Tue, 02 Aug 2022 17:06:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:06:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:06:27: 1000000 INFO @ Tue, 02 Aug 2022 17:06:36: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:06:46: 3000000 INFO @ Tue, 02 Aug 2022 17:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.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 @ Tue, 02 Aug 2022 17:06:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:06:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:06:57: 4000000 INFO @ Tue, 02 Aug 2022 17:06:59: 1000000 INFO @ Tue, 02 Aug 2022 17:07:09: 5000000 INFO @ Tue, 02 Aug 2022 17:07:10: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:07:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.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 @ Tue, 02 Aug 2022 17:07:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:07:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:07:20: 6000000 INFO @ Tue, 02 Aug 2022 17:07:22: 3000000 INFO @ Tue, 02 Aug 2022 17:07:29: 1000000 INFO @ Tue, 02 Aug 2022 17:07:32: 7000000 INFO @ Tue, 02 Aug 2022 17:07:34: 4000000 INFO @ Tue, 02 Aug 2022 17:07:41: 2000000 INFO @ Tue, 02 Aug 2022 17:07:44: 8000000 INFO @ Tue, 02 Aug 2022 17:07:46: 5000000 INFO @ Tue, 02 Aug 2022 17:07:53: 3000000 INFO @ Tue, 02 Aug 2022 17:07:55: 9000000 INFO @ Tue, 02 Aug 2022 17:07:57: 6000000 INFO @ Tue, 02 Aug 2022 17:08:05: 4000000 INFO @ Tue, 02 Aug 2022 17:08:07: 10000000 INFO @ Tue, 02 Aug 2022 17:08:09: 7000000 INFO @ Tue, 02 Aug 2022 17:08:17: 5000000 INFO @ Tue, 02 Aug 2022 17:08:18: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:08:20: 8000000 INFO @ Tue, 02 Aug 2022 17:08:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:08:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:08:21: #1 total tags in treatment: 4232549 INFO @ Tue, 02 Aug 2022 17:08:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:08:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:08:21: #1 tags after filtering in treatment: 3322291 INFO @ Tue, 02 Aug 2022 17:08:21: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:08:21: #1 finished! INFO @ Tue, 02 Aug 2022 17:08:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:08:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:08:22: #2 number of paired peaks: 4573 INFO @ Tue, 02 Aug 2022 17:08:22: start model_add_line... INFO @ Tue, 02 Aug 2022 17:08:22: start X-correlation... INFO @ Tue, 02 Aug 2022 17:08:22: end of X-cor INFO @ Tue, 02 Aug 2022 17:08:22: #2 finished! INFO @ Tue, 02 Aug 2022 17:08:22: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 17:08:22: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 17:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.05_model.r WARNING @ Tue, 02 Aug 2022 17:08:22: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:08:22: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 17:08:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:08:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:08:28: 6000000 INFO @ Tue, 02 Aug 2022 17:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:08:31: 9000000 INFO @ Tue, 02 Aug 2022 17:08:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:08:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:08:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.05_summits.bed INFO @ Tue, 02 Aug 2022 17:08:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7145 records, 4 fields): 43 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:08:39: 7000000 INFO @ Tue, 02 Aug 2022 17:08:42: 10000000 INFO @ Tue, 02 Aug 2022 17:08:50: 8000000 INFO @ Tue, 02 Aug 2022 17:08:53: 11000000 INFO @ Tue, 02 Aug 2022 17:08:56: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:08:56: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:08:56: #1 total tags in treatment: 4232549 INFO @ Tue, 02 Aug 2022 17:08:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:08:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:08:56: #1 tags after filtering in treatment: 3322291 INFO @ Tue, 02 Aug 2022 17:08:56: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:08:56: #1 finished! INFO @ Tue, 02 Aug 2022 17:08:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:08:57: #2 number of paired peaks: 4573 INFO @ Tue, 02 Aug 2022 17:08:57: start model_add_line... INFO @ Tue, 02 Aug 2022 17:08:57: start X-correlation... INFO @ Tue, 02 Aug 2022 17:08:57: end of X-cor INFO @ Tue, 02 Aug 2022 17:08:57: #2 finished! INFO @ Tue, 02 Aug 2022 17:08:57: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 17:08:57: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 17:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.10_model.r WARNING @ Tue, 02 Aug 2022 17:08:57: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:08:57: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 17:08:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:08:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:09:01: 9000000 INFO @ Tue, 02 Aug 2022 17:09:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.10_summits.bed INFO @ Tue, 02 Aug 2022 17:09:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4519 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:09:11: 10000000 INFO @ Tue, 02 Aug 2022 17:09:21: 11000000 INFO @ Tue, 02 Aug 2022 17:09:24: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:09:24: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:09:24: #1 total tags in treatment: 4232549 INFO @ Tue, 02 Aug 2022 17:09:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:09:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:09:24: #1 tags after filtering in treatment: 3322291 INFO @ Tue, 02 Aug 2022 17:09:24: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:09:24: #1 finished! INFO @ Tue, 02 Aug 2022 17:09:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:09:24: #2 number of paired peaks: 4573 INFO @ Tue, 02 Aug 2022 17:09:24: start model_add_line... INFO @ Tue, 02 Aug 2022 17:09:24: start X-correlation... INFO @ Tue, 02 Aug 2022 17:09:24: end of X-cor INFO @ Tue, 02 Aug 2022 17:09:24: #2 finished! INFO @ Tue, 02 Aug 2022 17:09:24: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 17:09:24: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 17:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.20_model.r WARNING @ Tue, 02 Aug 2022 17:09:24: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:09:24: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 17:09:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:09:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:09:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175826/SRX12175826.20_summits.bed INFO @ Tue, 02 Aug 2022 17:09:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2252 records, 4 fields): 38 millis CompletedMACS2peakCalling