Job ID = 14168393 SRX = ERX3978748 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22359474 spots for ERR3975759/ERR3975759.sra Written 22359474 spots for ERR3975759/ERR3975759.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169679 ("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: 00:50:39 22359474 reads; of these: 22359474 (100.00%) were paired; of these: 10017923 (44.80%) aligned concordantly 0 times 3391503 (15.17%) aligned concordantly exactly 1 time 8950048 (40.03%) aligned concordantly >1 times ---- 10017923 pairs aligned concordantly 0 times; of these: 1146707 (11.45%) aligned discordantly 1 time ---- 8871216 pairs aligned 0 times concordantly or discordantly; of these: 17742432 mates make up the pairs; of these: 9972233 (56.21%) aligned 0 times 339497 (1.91%) aligned exactly 1 time 7430702 (41.88%) aligned >1 times 77.70% overall alignment rate Time searching: 00:50:39 Overall time: 00:50:39 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 24 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] 7474977 / 13340890 = 0.5603 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 19:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.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 19:24:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:24:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:24:16: 1000000 INFO @ Fri, 10 Dec 2021 19:24:23: 2000000 INFO @ Fri, 10 Dec 2021 19:24:30: 3000000 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 19:24:37: 4000000 INFO @ Fri, 10 Dec 2021 19:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.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 19:24:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:24:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:24:44: 5000000 INFO @ Fri, 10 Dec 2021 19:24:45: 1000000 INFO @ Fri, 10 Dec 2021 19:24:52: 6000000 INFO @ Fri, 10 Dec 2021 19:24:52: 2000000 INFO @ Fri, 10 Dec 2021 19:24:59: 7000000 INFO @ Fri, 10 Dec 2021 19:24:59: 3000000 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 19:25:06: 8000000 INFO @ Fri, 10 Dec 2021 19:25:06: 4000000 INFO @ Fri, 10 Dec 2021 19:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.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 19:25:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:25:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:25:13: 9000000 INFO @ Fri, 10 Dec 2021 19:25:14: 5000000 INFO @ Fri, 10 Dec 2021 19:25:16: 1000000 INFO @ Fri, 10 Dec 2021 19:25:19: 10000000 INFO @ Fri, 10 Dec 2021 19:25:22: 6000000 INFO @ Fri, 10 Dec 2021 19:25:25: 2000000 INFO @ Fri, 10 Dec 2021 19:25:26: 11000000 INFO @ Fri, 10 Dec 2021 19:25:29: 7000000 INFO @ Fri, 10 Dec 2021 19:25:33: 12000000 INFO @ Fri, 10 Dec 2021 19:25:33: 3000000 INFO @ Fri, 10 Dec 2021 19:25:37: 8000000 INFO @ Fri, 10 Dec 2021 19:25:40: 13000000 INFO @ Fri, 10 Dec 2021 19:25:42: 4000000 INFO @ Fri, 10 Dec 2021 19:25:44: 9000000 INFO @ Fri, 10 Dec 2021 19:25:47: 14000000 INFO @ Fri, 10 Dec 2021 19:25:50: 10000000 INFO @ Fri, 10 Dec 2021 19:25:52: 5000000 INFO @ Fri, 10 Dec 2021 19:25:54: 15000000 INFO @ Fri, 10 Dec 2021 19:25:57: 11000000 INFO @ Fri, 10 Dec 2021 19:26:00: 6000000 INFO @ Fri, 10 Dec 2021 19:26:00: 16000000 INFO @ Fri, 10 Dec 2021 19:26:04: 12000000 INFO @ Fri, 10 Dec 2021 19:26:07: 17000000 INFO @ Fri, 10 Dec 2021 19:26:08: 7000000 INFO @ Fri, 10 Dec 2021 19:26:11: 13000000 INFO @ Fri, 10 Dec 2021 19:26:14: 18000000 INFO @ Fri, 10 Dec 2021 19:26:16: 8000000 INFO @ Fri, 10 Dec 2021 19:26:18: 14000000 INFO @ Fri, 10 Dec 2021 19:26:22: 19000000 INFO @ Fri, 10 Dec 2021 19:26:23: 9000000 INFO @ Fri, 10 Dec 2021 19:26:25: 15000000 INFO @ Fri, 10 Dec 2021 19:26:28: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:26:28: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:26:28: #1 total tags in treatment: 4955709 INFO @ Fri, 10 Dec 2021 19:26:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:26:28: #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 19:26:28: #1 tags after filtering in treatment: 3556188 INFO @ Fri, 10 Dec 2021 19:26:28: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 19:26:28: #1 finished! INFO @ Fri, 10 Dec 2021 19:26:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:26:28: #2 number of paired peaks: 2853 INFO @ Fri, 10 Dec 2021 19:26:28: start model_add_line... INFO @ Fri, 10 Dec 2021 19:26:28: start X-correlation... INFO @ Fri, 10 Dec 2021 19:26:28: end of X-cor INFO @ Fri, 10 Dec 2021 19:26:28: #2 finished! INFO @ Fri, 10 Dec 2021 19:26:28: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 19:26:28: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 19:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.05_model.r WARNING @ Fri, 10 Dec 2021 19:26:28: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:26:28: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 19:26:28: #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 19:26:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:26:31: 10000000 INFO @ Fri, 10 Dec 2021 19:26:32: 16000000 INFO @ Fri, 10 Dec 2021 19:26:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:26:38: 11000000 INFO @ Fri, 10 Dec 2021 19:26:40: 17000000 INFO @ Fri, 10 Dec 2021 19:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.05_summits.bed INFO @ Fri, 10 Dec 2021 19:26:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6436 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:26:45: 12000000 INFO @ Fri, 10 Dec 2021 19:26:48: 18000000 INFO @ Fri, 10 Dec 2021 19:26:53: 13000000 INFO @ Fri, 10 Dec 2021 19:26:56: 19000000 INFO @ Fri, 10 Dec 2021 19:27:00: 14000000 INFO @ Fri, 10 Dec 2021 19:27:02: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:27:02: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:27:02: #1 total tags in treatment: 4955709 INFO @ Fri, 10 Dec 2021 19:27:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:27:02: #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 19:27:02: #1 tags after filtering in treatment: 3556188 INFO @ Fri, 10 Dec 2021 19:27:02: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 19:27:02: #1 finished! INFO @ Fri, 10 Dec 2021 19:27:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:27:02: #2 number of paired peaks: 2853 INFO @ Fri, 10 Dec 2021 19:27:02: start model_add_line... INFO @ Fri, 10 Dec 2021 19:27:02: start X-correlation... INFO @ Fri, 10 Dec 2021 19:27:03: end of X-cor INFO @ Fri, 10 Dec 2021 19:27:03: #2 finished! INFO @ Fri, 10 Dec 2021 19:27:03: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 19:27:03: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 19:27:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.10_model.r WARNING @ Fri, 10 Dec 2021 19:27:03: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:27:03: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 19:27:03: #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 19:27:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:27:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:27:06: 15000000 INFO @ Fri, 10 Dec 2021 19:27:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:27:13: 16000000 INFO @ Fri, 10 Dec 2021 19:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.10_summits.bed INFO @ Fri, 10 Dec 2021 19:27:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3025 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:27:19: 17000000 INFO @ Fri, 10 Dec 2021 19:27:26: 18000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:27:33: 19000000 INFO @ Fri, 10 Dec 2021 19:27:38: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:27:38: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:27:38: #1 total tags in treatment: 4955709 INFO @ Fri, 10 Dec 2021 19:27:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:27:38: #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 19:27:39: #1 tags after filtering in treatment: 3556188 INFO @ Fri, 10 Dec 2021 19:27:39: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 19:27:39: #1 finished! INFO @ Fri, 10 Dec 2021 19:27:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:27:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:27:39: #2 number of paired peaks: 2853 INFO @ Fri, 10 Dec 2021 19:27:39: start model_add_line... INFO @ Fri, 10 Dec 2021 19:27:39: start X-correlation... INFO @ Fri, 10 Dec 2021 19:27:39: end of X-cor INFO @ Fri, 10 Dec 2021 19:27:39: #2 finished! INFO @ Fri, 10 Dec 2021 19:27:39: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 19:27:39: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 19:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.20_model.r WARNING @ Fri, 10 Dec 2021 19:27:39: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:27:39: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 19:27:39: #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 19:27:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:27:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978748/ERX3978748.20_summits.bed INFO @ Fri, 10 Dec 2021 19:27:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (797 records, 4 fields): 3 millis CompletedMACS2peakCalling