Job ID = 14168121 SRX = ERX3978946 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28626266 spots for ERR3976016/ERR3976016.sra Written 28626266 spots for ERR3976016/ERR3976016.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169152 ("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: 01:25:12 28626266 reads; of these: 28626266 (100.00%) were paired; of these: 10093981 (35.26%) aligned concordantly 0 times 14577540 (50.92%) aligned concordantly exactly 1 time 3954745 (13.82%) aligned concordantly >1 times ---- 10093981 pairs aligned concordantly 0 times; of these: 1197550 (11.86%) aligned discordantly 1 time ---- 8896431 pairs aligned 0 times concordantly or discordantly; of these: 17792862 mates make up the pairs; of these: 9295035 (52.24%) aligned 0 times 5155237 (28.97%) aligned exactly 1 time 3342590 (18.79%) aligned >1 times 83.76% overall alignment rate Time searching: 01:25:12 Overall time: 01:25:12 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 20 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] 14432595 / 19338236 = 0.7463 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 17:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.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 17:08:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:08:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:08:56: 1000000 INFO @ Fri, 10 Dec 2021 17:09:01: 2000000 INFO @ Fri, 10 Dec 2021 17:09:06: 3000000 INFO @ Fri, 10 Dec 2021 17:09:11: 4000000 INFO @ Fri, 10 Dec 2021 17:09:17: 5000000 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 17:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.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 17:09:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:09:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:09:22: 6000000 INFO @ Fri, 10 Dec 2021 17:09:26: 1000000 INFO @ Fri, 10 Dec 2021 17:09:28: 7000000 INFO @ Fri, 10 Dec 2021 17:09:33: 2000000 INFO @ Fri, 10 Dec 2021 17:09:35: 8000000 INFO @ Fri, 10 Dec 2021 17:09:39: 3000000 INFO @ Fri, 10 Dec 2021 17:09:41: 9000000 INFO @ Fri, 10 Dec 2021 17:09:45: 4000000 INFO @ Fri, 10 Dec 2021 17:09:47: 10000000 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 17:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.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 17:09:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:09:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:09:51: 5000000 INFO @ Fri, 10 Dec 2021 17:09:53: 11000000 INFO @ Fri, 10 Dec 2021 17:09:56: 1000000 INFO @ Fri, 10 Dec 2021 17:09:57: 6000000 INFO @ Fri, 10 Dec 2021 17:09:59: 12000000 INFO @ Fri, 10 Dec 2021 17:10:03: 2000000 INFO @ Fri, 10 Dec 2021 17:10:03: 7000000 INFO @ Fri, 10 Dec 2021 17:10:06: 13000000 INFO @ Fri, 10 Dec 2021 17:10:09: 3000000 INFO @ Fri, 10 Dec 2021 17:10:10: 8000000 INFO @ Fri, 10 Dec 2021 17:10:12: 14000000 INFO @ Fri, 10 Dec 2021 17:10:15: 4000000 INFO @ Fri, 10 Dec 2021 17:10:16: 9000000 INFO @ Fri, 10 Dec 2021 17:10:18: 15000000 INFO @ Fri, 10 Dec 2021 17:10:21: 5000000 INFO @ Fri, 10 Dec 2021 17:10:22: 10000000 INFO @ Fri, 10 Dec 2021 17:10:25: 16000000 INFO @ Fri, 10 Dec 2021 17:10:27: 6000000 INFO @ Fri, 10 Dec 2021 17:10:28: 11000000 INFO @ Fri, 10 Dec 2021 17:10:31: 17000000 INFO @ Fri, 10 Dec 2021 17:10:33: 7000000 INFO @ Fri, 10 Dec 2021 17:10:34: 12000000 INFO @ Fri, 10 Dec 2021 17:10:37: 18000000 INFO @ Fri, 10 Dec 2021 17:10:40: 8000000 INFO @ Fri, 10 Dec 2021 17:10:41: 13000000 INFO @ Fri, 10 Dec 2021 17:10:44: 19000000 INFO @ Fri, 10 Dec 2021 17:10:44: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:10:44: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:10:44: #1 total tags in treatment: 4773012 INFO @ Fri, 10 Dec 2021 17:10:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:10:44: #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 17:10:44: #1 tags after filtering in treatment: 4368981 INFO @ Fri, 10 Dec 2021 17:10:44: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:10:44: #1 finished! INFO @ Fri, 10 Dec 2021 17:10:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:10:45: #2 number of paired peaks: 1207 INFO @ Fri, 10 Dec 2021 17:10:45: start model_add_line... INFO @ Fri, 10 Dec 2021 17:10:45: start X-correlation... INFO @ Fri, 10 Dec 2021 17:10:45: end of X-cor INFO @ Fri, 10 Dec 2021 17:10:45: #2 finished! INFO @ Fri, 10 Dec 2021 17:10:45: #2 predicted fragment length is 143 bps INFO @ Fri, 10 Dec 2021 17:10:45: #2 alternative fragment length(s) may be 143 bps INFO @ Fri, 10 Dec 2021 17:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.05_model.r WARNING @ Fri, 10 Dec 2021 17:10:45: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:10:45: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Fri, 10 Dec 2021 17:10:45: #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 17:10:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:10:46: 9000000 INFO @ Fri, 10 Dec 2021 17:10:47: 14000000 INFO @ Fri, 10 Dec 2021 17:10:52: 10000000 INFO @ Fri, 10 Dec 2021 17:10:53: 15000000 INFO @ Fri, 10 Dec 2021 17:10:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:10:58: 11000000 INFO @ Fri, 10 Dec 2021 17:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.05_summits.bed INFO @ Fri, 10 Dec 2021 17:10:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4544 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:11:00: 16000000 INFO @ Fri, 10 Dec 2021 17:11:04: 12000000 INFO @ Fri, 10 Dec 2021 17:11:06: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:11:10: 13000000 INFO @ Fri, 10 Dec 2021 17:11:12: 18000000 INFO @ Fri, 10 Dec 2021 17:11:17: 14000000 INFO @ Fri, 10 Dec 2021 17:11:18: 19000000 INFO @ Fri, 10 Dec 2021 17:11:19: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:11:19: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:11:19: #1 total tags in treatment: 4773012 INFO @ Fri, 10 Dec 2021 17:11:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:11:19: #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 17:11:19: #1 tags after filtering in treatment: 4368981 INFO @ Fri, 10 Dec 2021 17:11:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:11:19: #1 finished! INFO @ Fri, 10 Dec 2021 17:11:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:11:19: #2 number of paired peaks: 1207 INFO @ Fri, 10 Dec 2021 17:11:19: start model_add_line... INFO @ Fri, 10 Dec 2021 17:11:19: start X-correlation... INFO @ Fri, 10 Dec 2021 17:11:19: end of X-cor INFO @ Fri, 10 Dec 2021 17:11:19: #2 finished! INFO @ Fri, 10 Dec 2021 17:11:19: #2 predicted fragment length is 143 bps INFO @ Fri, 10 Dec 2021 17:11:19: #2 alternative fragment length(s) may be 143 bps INFO @ Fri, 10 Dec 2021 17:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.10_model.r WARNING @ Fri, 10 Dec 2021 17:11:19: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:11:19: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Fri, 10 Dec 2021 17:11:19: #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 17:11:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:11:23: 15000000 INFO @ Fri, 10 Dec 2021 17:11:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:11:29: 16000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.10_summits.bed INFO @ Fri, 10 Dec 2021 17:11:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1797 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:11:35: 17000000 INFO @ Fri, 10 Dec 2021 17:11:41: 18000000 INFO @ Fri, 10 Dec 2021 17:11:46: 19000000 INFO @ Fri, 10 Dec 2021 17:11:47: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 17:11:47: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 17:11:47: #1 total tags in treatment: 4773012 INFO @ Fri, 10 Dec 2021 17:11:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:11:47: #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 17:11:47: #1 tags after filtering in treatment: 4368981 INFO @ Fri, 10 Dec 2021 17:11:47: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 17:11:47: #1 finished! INFO @ Fri, 10 Dec 2021 17:11:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:11:47: #2 number of paired peaks: 1207 INFO @ Fri, 10 Dec 2021 17:11:47: start model_add_line... INFO @ Fri, 10 Dec 2021 17:11:47: start X-correlation... INFO @ Fri, 10 Dec 2021 17:11:47: end of X-cor INFO @ Fri, 10 Dec 2021 17:11:47: #2 finished! INFO @ Fri, 10 Dec 2021 17:11:47: #2 predicted fragment length is 143 bps INFO @ Fri, 10 Dec 2021 17:11:47: #2 alternative fragment length(s) may be 143 bps INFO @ Fri, 10 Dec 2021 17:11:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.20_model.r WARNING @ Fri, 10 Dec 2021 17:11:47: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:11:47: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Fri, 10 Dec 2021 17:11:47: #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 17:11:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:11:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978946/ERX3978946.20_summits.bed INFO @ Fri, 10 Dec 2021 17:12:01: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling