Job ID = 14170077 SRX = SRX8556367 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30028352 spots for SRR12024923/SRR12024923.sra Written 30028352 spots for SRR12024923/SRR12024923.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170715 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:56:03 30028352 reads; of these: 30028352 (100.00%) were paired; of these: 21372718 (71.18%) aligned concordantly 0 times 6180210 (20.58%) aligned concordantly exactly 1 time 2475424 (8.24%) aligned concordantly >1 times ---- 21372718 pairs aligned concordantly 0 times; of these: 940948 (4.40%) aligned discordantly 1 time ---- 20431770 pairs aligned 0 times concordantly or discordantly; of these: 40863540 mates make up the pairs; of these: 39803372 (97.41%) aligned 0 times 289028 (0.71%) aligned exactly 1 time 771140 (1.89%) aligned >1 times 33.72% overall alignment rate Time searching: 00:56:04 Overall time: 00:56:04 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 16 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] 6628953 / 9529035 = 0.6957 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 @ Sat, 11 Dec 2021 06:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.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, 11 Dec 2021 06:15:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:15:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:15:48: 1000000 INFO @ Sat, 11 Dec 2021 06:15:59: 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 @ Sat, 11 Dec 2021 06:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.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, 11 Dec 2021 06:16:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:16:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:16:10: 3000000 INFO @ Sat, 11 Dec 2021 06:16:21: 4000000 INFO @ Sat, 11 Dec 2021 06:16:26: 1000000 INFO @ Sat, 11 Dec 2021 06:16:32: 5000000 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 @ Sat, 11 Dec 2021 06:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.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, 11 Dec 2021 06:16:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:16:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:16:44: 6000000 INFO @ Sat, 11 Dec 2021 06:16:44: 2000000 INFO @ Sat, 11 Dec 2021 06:16:50: 1000000 INFO @ Sat, 11 Dec 2021 06:16:55: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:16:55: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:16:55: #1 total tags in treatment: 2509615 INFO @ Sat, 11 Dec 2021 06:16:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:16:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:16:55: #1 tags after filtering in treatment: 2263951 INFO @ Sat, 11 Dec 2021 06:16:55: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 06:16:55: #1 finished! INFO @ Sat, 11 Dec 2021 06:16:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:16:56: #2 number of paired peaks: 2852 INFO @ Sat, 11 Dec 2021 06:16:56: start model_add_line... INFO @ Sat, 11 Dec 2021 06:16:56: start X-correlation... INFO @ Sat, 11 Dec 2021 06:16:56: end of X-cor INFO @ Sat, 11 Dec 2021 06:16:56: #2 finished! INFO @ Sat, 11 Dec 2021 06:16:56: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 06:16:56: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 06:16:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.05_model.r WARNING @ Sat, 11 Dec 2021 06:16:56: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:16:56: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 06:16:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:16:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:16:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:17:02: 3000000 INFO @ Sat, 11 Dec 2021 06:17:03: 2000000 INFO @ Sat, 11 Dec 2021 06:17:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:17:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:17:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:17:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.05_summits.bed INFO @ Sat, 11 Dec 2021 06:17:08: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5598 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:17:16: 3000000 INFO @ Sat, 11 Dec 2021 06:17:20: 4000000 INFO @ Sat, 11 Dec 2021 06:17:29: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:17:37: 5000000 INFO @ Sat, 11 Dec 2021 06:17:42: 5000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:17:55: 6000000 INFO @ Sat, 11 Dec 2021 06:17:56: 6000000 INFO @ Sat, 11 Dec 2021 06:18:07: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:18:07: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:18:07: #1 total tags in treatment: 2509615 INFO @ Sat, 11 Dec 2021 06:18:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:18:07: #1 tags after filtering in treatment: 2263951 INFO @ Sat, 11 Dec 2021 06:18:07: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 06:18:07: #1 finished! INFO @ Sat, 11 Dec 2021 06:18:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:18:08: #2 number of paired peaks: 2852 INFO @ Sat, 11 Dec 2021 06:18:08: start model_add_line... INFO @ Sat, 11 Dec 2021 06:18:08: start X-correlation... INFO @ Sat, 11 Dec 2021 06:18:08: end of X-cor INFO @ Sat, 11 Dec 2021 06:18:08: #2 finished! INFO @ Sat, 11 Dec 2021 06:18:08: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 06:18:08: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 06:18:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.20_model.r WARNING @ Sat, 11 Dec 2021 06:18:08: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:18:08: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 06:18:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:18:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:18:14: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:18:14: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:18:14: #1 total tags in treatment: 2509615 INFO @ Sat, 11 Dec 2021 06:18:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:18:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:18:14: #1 tags after filtering in treatment: 2263951 INFO @ Sat, 11 Dec 2021 06:18:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 11 Dec 2021 06:18:14: #1 finished! INFO @ Sat, 11 Dec 2021 06:18:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:18:14: #2 number of paired peaks: 2852 INFO @ Sat, 11 Dec 2021 06:18:14: start model_add_line... INFO @ Sat, 11 Dec 2021 06:18:14: start X-correlation... INFO @ Sat, 11 Dec 2021 06:18:14: end of X-cor INFO @ Sat, 11 Dec 2021 06:18:14: #2 finished! INFO @ Sat, 11 Dec 2021 06:18:14: #2 predicted fragment length is 201 bps INFO @ Sat, 11 Dec 2021 06:18:14: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 11 Dec 2021 06:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.10_model.r WARNING @ Sat, 11 Dec 2021 06:18:14: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:18:14: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 11 Dec 2021 06:18:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:18:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:18:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:18:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.20_summits.bed INFO @ Sat, 11 Dec 2021 06:18:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:18:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556367/SRX8556367.10_summits.bed INFO @ Sat, 11 Dec 2021 06:18:27: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2824 records, 4 fields): 7 millis CompletedMACS2peakCalling