Job ID = 14171982 SRX = SRX10089729 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17751851 spots for SRR13700616/SRR13700616.sra Written 17751851 spots for SRR13700616/SRR13700616.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172577 ("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: 00:44:19 17751851 reads; of these: 17751851 (100.00%) were paired; of these: 3732554 (21.03%) aligned concordantly 0 times 10790348 (60.78%) aligned concordantly exactly 1 time 3228949 (18.19%) aligned concordantly >1 times ---- 3732554 pairs aligned concordantly 0 times; of these: 147432 (3.95%) aligned discordantly 1 time ---- 3585122 pairs aligned 0 times concordantly or discordantly; of these: 7170244 mates make up the pairs; of these: 6381599 (89.00%) aligned 0 times 430695 (6.01%) aligned exactly 1 time 357950 (4.99%) aligned >1 times 82.03% overall alignment rate Time searching: 00:44:19 Overall time: 00:44:19 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] 2558932 / 10387593 = 0.2463 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 14:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.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 14:37:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:37:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:37:34: 1000000 INFO @ Sat, 11 Dec 2021 14:37:41: 2000000 INFO @ Sat, 11 Dec 2021 14:37:47: 3000000 INFO @ Sat, 11 Dec 2021 14:37:54: 4000000 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 14:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.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 14:37:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:37:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:38:00: 5000000 INFO @ Sat, 11 Dec 2021 14:38:04: 1000000 INFO @ Sat, 11 Dec 2021 14:38:07: 6000000 INFO @ Sat, 11 Dec 2021 14:38:11: 2000000 INFO @ Sat, 11 Dec 2021 14:38:13: 7000000 INFO @ Sat, 11 Dec 2021 14:38:18: 3000000 INFO @ Sat, 11 Dec 2021 14:38:20: 8000000 INFO @ Sat, 11 Dec 2021 14:38:24: 4000000 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 14:38:27: 9000000 INFO @ Sat, 11 Dec 2021 14:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.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 14:38:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:38:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:38:31: 5000000 INFO @ Sat, 11 Dec 2021 14:38:34: 10000000 INFO @ Sat, 11 Dec 2021 14:38:34: 1000000 INFO @ Sat, 11 Dec 2021 14:38:37: 6000000 INFO @ Sat, 11 Dec 2021 14:38:41: 11000000 INFO @ Sat, 11 Dec 2021 14:38:41: 2000000 INFO @ Sat, 11 Dec 2021 14:38:44: 7000000 INFO @ Sat, 11 Dec 2021 14:38:47: 12000000 INFO @ Sat, 11 Dec 2021 14:38:48: 3000000 INFO @ Sat, 11 Dec 2021 14:38:51: 8000000 INFO @ Sat, 11 Dec 2021 14:38:54: 13000000 INFO @ Sat, 11 Dec 2021 14:38:54: 4000000 INFO @ Sat, 11 Dec 2021 14:38:57: 9000000 INFO @ Sat, 11 Dec 2021 14:39:00: 14000000 INFO @ Sat, 11 Dec 2021 14:39:00: 5000000 INFO @ Sat, 11 Dec 2021 14:39:04: 10000000 INFO @ Sat, 11 Dec 2021 14:39:06: 15000000 INFO @ Sat, 11 Dec 2021 14:39:06: 6000000 INFO @ Sat, 11 Dec 2021 14:39:10: 11000000 INFO @ Sat, 11 Dec 2021 14:39:12: 16000000 INFO @ Sat, 11 Dec 2021 14:39:13: 7000000 INFO @ Sat, 11 Dec 2021 14:39:16: 12000000 INFO @ Sat, 11 Dec 2021 14:39:18: 17000000 INFO @ Sat, 11 Dec 2021 14:39:19: 8000000 INFO @ Sat, 11 Dec 2021 14:39:23: 13000000 INFO @ Sat, 11 Dec 2021 14:39:24: 18000000 INFO @ Sat, 11 Dec 2021 14:39:25: 9000000 INFO @ Sat, 11 Dec 2021 14:39:29: 14000000 INFO @ Sat, 11 Dec 2021 14:39:30: 19000000 INFO @ Sat, 11 Dec 2021 14:39:31: 10000000 INFO @ Sat, 11 Dec 2021 14:39:36: 15000000 INFO @ Sat, 11 Dec 2021 14:39:37: 20000000 INFO @ Sat, 11 Dec 2021 14:39:37: 11000000 INFO @ Sat, 11 Dec 2021 14:39:42: 16000000 INFO @ Sat, 11 Dec 2021 14:39:43: 12000000 INFO @ Sat, 11 Dec 2021 14:39:44: 21000000 INFO @ Sat, 11 Dec 2021 14:39:49: 17000000 INFO @ Sat, 11 Dec 2021 14:39:49: 13000000 INFO @ Sat, 11 Dec 2021 14:39:50: 22000000 INFO @ Sat, 11 Dec 2021 14:39:55: 14000000 INFO @ Sat, 11 Dec 2021 14:39:56: 18000000 INFO @ Sat, 11 Dec 2021 14:39:56: 23000000 INFO @ Sat, 11 Dec 2021 14:40:02: 15000000 INFO @ Sat, 11 Dec 2021 14:40:02: 24000000 INFO @ Sat, 11 Dec 2021 14:40:02: 19000000 INFO @ Sat, 11 Dec 2021 14:40:03: #1 tag size is determined as 70 bps INFO @ Sat, 11 Dec 2021 14:40:03: #1 tag size = 70 INFO @ Sat, 11 Dec 2021 14:40:03: #1 total tags in treatment: 11463454 INFO @ Sat, 11 Dec 2021 14:40:03: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:40:03: #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 14:40:03: #1 tags after filtering in treatment: 7568711 INFO @ Sat, 11 Dec 2021 14:40:03: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:40:03: #1 finished! INFO @ Sat, 11 Dec 2021 14:40:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:40:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:40:04: #2 number of paired peaks: 3112 INFO @ Sat, 11 Dec 2021 14:40:04: start model_add_line... INFO @ Sat, 11 Dec 2021 14:40:04: start X-correlation... INFO @ Sat, 11 Dec 2021 14:40:04: end of X-cor INFO @ Sat, 11 Dec 2021 14:40:04: #2 finished! INFO @ Sat, 11 Dec 2021 14:40:04: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 14:40:04: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 14:40:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.05_model.r WARNING @ Sat, 11 Dec 2021 14:40:04: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:40:04: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sat, 11 Dec 2021 14:40:04: #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 14:40:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:40:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:40:07: 16000000 INFO @ Sat, 11 Dec 2021 14:40:09: 20000000 INFO @ Sat, 11 Dec 2021 14:40:13: 17000000 INFO @ Sat, 11 Dec 2021 14:40:16: 21000000 INFO @ Sat, 11 Dec 2021 14:40:19: 18000000 INFO @ Sat, 11 Dec 2021 14:40:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:40:22: 22000000 INFO @ Sat, 11 Dec 2021 14:40:24: 19000000 INFO @ Sat, 11 Dec 2021 14:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.05_summits.bed INFO @ Sat, 11 Dec 2021 14:40:29: Done! INFO @ Sat, 11 Dec 2021 14:40:29: 23000000 pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14435 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:40:30: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:40:35: 24000000 INFO @ Sat, 11 Dec 2021 14:40:36: 21000000 INFO @ Sat, 11 Dec 2021 14:40:36: #1 tag size is determined as 70 bps INFO @ Sat, 11 Dec 2021 14:40:36: #1 tag size = 70 INFO @ Sat, 11 Dec 2021 14:40:36: #1 total tags in treatment: 11463454 INFO @ Sat, 11 Dec 2021 14:40:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:40:36: #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 14:40:36: #1 tags after filtering in treatment: 7568711 INFO @ Sat, 11 Dec 2021 14:40:36: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:40:36: #1 finished! INFO @ Sat, 11 Dec 2021 14:40:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:40:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:40:37: #2 number of paired peaks: 3112 INFO @ Sat, 11 Dec 2021 14:40:37: start model_add_line... INFO @ Sat, 11 Dec 2021 14:40:37: start X-correlation... INFO @ Sat, 11 Dec 2021 14:40:37: end of X-cor INFO @ Sat, 11 Dec 2021 14:40:37: #2 finished! INFO @ Sat, 11 Dec 2021 14:40:37: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 14:40:37: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 14:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.10_model.r WARNING @ Sat, 11 Dec 2021 14:40:37: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:40:37: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sat, 11 Dec 2021 14:40:37: #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 14:40:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:40:41: 22000000 INFO @ Sat, 11 Dec 2021 14:40:47: 23000000 INFO @ Sat, 11 Dec 2021 14:40:52: 24000000 INFO @ Sat, 11 Dec 2021 14:40:52: #1 tag size is determined as 70 bps INFO @ Sat, 11 Dec 2021 14:40:52: #1 tag size = 70 INFO @ Sat, 11 Dec 2021 14:40:52: #1 total tags in treatment: 11463454 INFO @ Sat, 11 Dec 2021 14:40:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:40:52: #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 14:40:53: #1 tags after filtering in treatment: 7568711 INFO @ Sat, 11 Dec 2021 14:40:53: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:40:53: #1 finished! INFO @ Sat, 11 Dec 2021 14:40:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:40:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:40:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:40:53: #2 number of paired peaks: 3112 INFO @ Sat, 11 Dec 2021 14:40:53: start model_add_line... INFO @ Sat, 11 Dec 2021 14:40:53: start X-correlation... INFO @ Sat, 11 Dec 2021 14:40:53: end of X-cor INFO @ Sat, 11 Dec 2021 14:40:53: #2 finished! INFO @ Sat, 11 Dec 2021 14:40:53: #2 predicted fragment length is 101 bps INFO @ Sat, 11 Dec 2021 14:40:53: #2 alternative fragment length(s) may be 101 bps INFO @ Sat, 11 Dec 2021 14:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.20_model.r WARNING @ Sat, 11 Dec 2021 14:40:53: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:40:53: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sat, 11 Dec 2021 14:40:53: #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 14:40:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.10_summits.bed INFO @ Sat, 11 Dec 2021 14:41:02: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (9011 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:41:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089729/SRX10089729.20_summits.bed INFO @ Sat, 11 Dec 2021 14:41:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4215 records, 4 fields): 7 millis CompletedMACS2peakCalling