Job ID = 12265504 SRX = SRX7277011 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23712831 spots for SRR10597276/SRR10597276.sra Written 23712831 spots for SRR10597276/SRR10597276.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265771 ("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: 00:36:20 23712831 reads; of these: 23712831 (100.00%) were paired; of these: 8765618 (36.97%) aligned concordantly 0 times 9342519 (39.40%) aligned concordantly exactly 1 time 5604694 (23.64%) aligned concordantly >1 times ---- 8765618 pairs aligned concordantly 0 times; of these: 2257571 (25.75%) aligned discordantly 1 time ---- 6508047 pairs aligned 0 times concordantly or discordantly; of these: 13016094 mates make up the pairs; of these: 9930517 (76.29%) aligned 0 times 644755 (4.95%) aligned exactly 1 time 2440822 (18.75%) aligned >1 times 79.06% overall alignment rate Time searching: 00:36:20 Overall time: 00:36:20 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] 3116469 / 17069698 = 0.1826 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.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, 03 Apr 2021 08:11:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:11:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:11:33: 1000000 INFO @ Sat, 03 Apr 2021 08:11:38: 2000000 INFO @ Sat, 03 Apr 2021 08:11:44: 3000000 INFO @ Sat, 03 Apr 2021 08:11:49: 4000000 INFO @ Sat, 03 Apr 2021 08:11:55: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:11:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.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, 03 Apr 2021 08:11:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:11:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:12:00: 6000000 INFO @ Sat, 03 Apr 2021 08:12:03: 1000000 INFO @ Sat, 03 Apr 2021 08:12:06: 7000000 INFO @ Sat, 03 Apr 2021 08:12:09: 2000000 INFO @ Sat, 03 Apr 2021 08:12:12: 8000000 INFO @ Sat, 03 Apr 2021 08:12:15: 3000000 INFO @ Sat, 03 Apr 2021 08:12:17: 9000000 INFO @ Sat, 03 Apr 2021 08:12:21: 4000000 INFO @ Sat, 03 Apr 2021 08:12:23: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:12:27: 5000000 INFO @ Sat, 03 Apr 2021 08:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.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, 03 Apr 2021 08:12:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:12:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:12:29: 11000000 INFO @ Sat, 03 Apr 2021 08:12:33: 6000000 INFO @ Sat, 03 Apr 2021 08:12:33: 1000000 INFO @ Sat, 03 Apr 2021 08:12:35: 12000000 INFO @ Sat, 03 Apr 2021 08:12:39: 7000000 INFO @ Sat, 03 Apr 2021 08:12:39: 2000000 INFO @ Sat, 03 Apr 2021 08:12:40: 13000000 INFO @ Sat, 03 Apr 2021 08:12:45: 3000000 INFO @ Sat, 03 Apr 2021 08:12:45: 8000000 INFO @ Sat, 03 Apr 2021 08:12:46: 14000000 INFO @ Sat, 03 Apr 2021 08:12:51: 4000000 INFO @ Sat, 03 Apr 2021 08:12:51: 9000000 INFO @ Sat, 03 Apr 2021 08:12:52: 15000000 INFO @ Sat, 03 Apr 2021 08:12:57: 10000000 INFO @ Sat, 03 Apr 2021 08:12:57: 5000000 INFO @ Sat, 03 Apr 2021 08:12:58: 16000000 INFO @ Sat, 03 Apr 2021 08:13:03: 6000000 INFO @ Sat, 03 Apr 2021 08:13:03: 11000000 INFO @ Sat, 03 Apr 2021 08:13:04: 17000000 INFO @ Sat, 03 Apr 2021 08:13:09: 7000000 INFO @ Sat, 03 Apr 2021 08:13:09: 12000000 INFO @ Sat, 03 Apr 2021 08:13:10: 18000000 INFO @ Sat, 03 Apr 2021 08:13:15: 8000000 INFO @ Sat, 03 Apr 2021 08:13:15: 13000000 INFO @ Sat, 03 Apr 2021 08:13:15: 19000000 INFO @ Sat, 03 Apr 2021 08:13:21: 9000000 INFO @ Sat, 03 Apr 2021 08:13:21: 14000000 INFO @ Sat, 03 Apr 2021 08:13:21: 20000000 INFO @ Sat, 03 Apr 2021 08:13:27: 10000000 INFO @ Sat, 03 Apr 2021 08:13:27: 15000000 INFO @ Sat, 03 Apr 2021 08:13:27: 21000000 INFO @ Sat, 03 Apr 2021 08:13:33: 11000000 INFO @ Sat, 03 Apr 2021 08:13:33: 16000000 INFO @ Sat, 03 Apr 2021 08:13:33: 22000000 INFO @ Sat, 03 Apr 2021 08:13:38: 12000000 INFO @ Sat, 03 Apr 2021 08:13:39: 17000000 INFO @ Sat, 03 Apr 2021 08:13:39: 23000000 INFO @ Sat, 03 Apr 2021 08:13:44: 13000000 INFO @ Sat, 03 Apr 2021 08:13:45: 24000000 INFO @ Sat, 03 Apr 2021 08:13:45: 18000000 INFO @ Sat, 03 Apr 2021 08:13:50: 14000000 INFO @ Sat, 03 Apr 2021 08:13:50: 25000000 INFO @ Sat, 03 Apr 2021 08:13:51: 19000000 INFO @ Sat, 03 Apr 2021 08:13:56: 26000000 INFO @ Sat, 03 Apr 2021 08:13:56: 15000000 INFO @ Sat, 03 Apr 2021 08:13:57: 20000000 INFO @ Sat, 03 Apr 2021 08:14:02: 16000000 INFO @ Sat, 03 Apr 2021 08:14:02: 27000000 INFO @ Sat, 03 Apr 2021 08:14:03: 21000000 INFO @ Sat, 03 Apr 2021 08:14:08: 17000000 INFO @ Sat, 03 Apr 2021 08:14:08: 28000000 INFO @ Sat, 03 Apr 2021 08:14:09: 22000000 INFO @ Sat, 03 Apr 2021 08:14:14: 18000000 INFO @ Sat, 03 Apr 2021 08:14:15: 29000000 INFO @ Sat, 03 Apr 2021 08:14:15: 23000000 INFO @ Sat, 03 Apr 2021 08:14:20: 19000000 INFO @ Sat, 03 Apr 2021 08:14:21: 30000000 INFO @ Sat, 03 Apr 2021 08:14:21: 24000000 INFO @ Sat, 03 Apr 2021 08:14:26: 20000000 INFO @ Sat, 03 Apr 2021 08:14:27: 31000000 INFO @ Sat, 03 Apr 2021 08:14:27: 25000000 INFO @ Sat, 03 Apr 2021 08:14:28: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:14:28: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:14:28: #1 total tags in treatment: 11925001 INFO @ Sat, 03 Apr 2021 08:14:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:14:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:14:28: #1 tags after filtering in treatment: 9596868 INFO @ Sat, 03 Apr 2021 08:14:28: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 08:14:28: #1 finished! INFO @ Sat, 03 Apr 2021 08:14:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:14:29: #2 number of paired peaks: 163 WARNING @ Sat, 03 Apr 2021 08:14:29: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 03 Apr 2021 08:14:29: start model_add_line... INFO @ Sat, 03 Apr 2021 08:14:29: start X-correlation... INFO @ Sat, 03 Apr 2021 08:14:29: end of X-cor INFO @ Sat, 03 Apr 2021 08:14:29: #2 finished! INFO @ Sat, 03 Apr 2021 08:14:29: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:14:29: #2 alternative fragment length(s) may be 3,97,100 bps INFO @ Sat, 03 Apr 2021 08:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.05_model.r WARNING @ Sat, 03 Apr 2021 08:14:29: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:14:29: #2 You may need to consider one of the other alternative d(s): 3,97,100 WARNING @ Sat, 03 Apr 2021 08:14:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:14:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:14:32: 21000000 INFO @ Sat, 03 Apr 2021 08:14:33: 26000000 INFO @ Sat, 03 Apr 2021 08:14:38: 22000000 INFO @ Sat, 03 Apr 2021 08:14:39: 27000000 INFO @ Sat, 03 Apr 2021 08:14:44: 23000000 INFO @ Sat, 03 Apr 2021 08:14:46: 28000000 INFO @ Sat, 03 Apr 2021 08:14:50: 24000000 INFO @ Sat, 03 Apr 2021 08:14:52: 29000000 INFO @ Sat, 03 Apr 2021 08:14:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:14:56: 25000000 INFO @ Sat, 03 Apr 2021 08:14:58: 30000000 INFO @ Sat, 03 Apr 2021 08:15:02: 26000000 INFO @ Sat, 03 Apr 2021 08:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.05_summits.bed INFO @ Sat, 03 Apr 2021 08:15:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4590 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:15:04: 31000000 INFO @ Sat, 03 Apr 2021 08:15:06: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:15:06: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:15:06: #1 total tags in treatment: 11925001 INFO @ Sat, 03 Apr 2021 08:15:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:15:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:15:06: #1 tags after filtering in treatment: 9596868 INFO @ Sat, 03 Apr 2021 08:15:06: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 08:15:06: #1 finished! INFO @ Sat, 03 Apr 2021 08:15:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:15:07: #2 number of paired peaks: 163 WARNING @ Sat, 03 Apr 2021 08:15:07: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 03 Apr 2021 08:15:07: start model_add_line... INFO @ Sat, 03 Apr 2021 08:15:07: start X-correlation... INFO @ Sat, 03 Apr 2021 08:15:07: end of X-cor INFO @ Sat, 03 Apr 2021 08:15:07: #2 finished! INFO @ Sat, 03 Apr 2021 08:15:07: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:15:07: #2 alternative fragment length(s) may be 3,97,100 bps INFO @ Sat, 03 Apr 2021 08:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.10_model.r WARNING @ Sat, 03 Apr 2021 08:15:07: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:15:07: #2 You may need to consider one of the other alternative d(s): 3,97,100 WARNING @ Sat, 03 Apr 2021 08:15:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:15:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:15:08: 27000000 INFO @ Sat, 03 Apr 2021 08:15:14: 28000000 INFO @ Sat, 03 Apr 2021 08:15:20: 29000000 INFO @ Sat, 03 Apr 2021 08:15:26: 30000000 INFO @ Sat, 03 Apr 2021 08:15:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:15:31: 31000000 INFO @ Sat, 03 Apr 2021 08:15:33: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:15:33: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:15:33: #1 total tags in treatment: 11925001 INFO @ Sat, 03 Apr 2021 08:15:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:15:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:15:33: #1 tags after filtering in treatment: 9596868 INFO @ Sat, 03 Apr 2021 08:15:33: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 03 Apr 2021 08:15:33: #1 finished! INFO @ Sat, 03 Apr 2021 08:15:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:15:34: #2 number of paired peaks: 163 WARNING @ Sat, 03 Apr 2021 08:15:34: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Sat, 03 Apr 2021 08:15:34: start model_add_line... INFO @ Sat, 03 Apr 2021 08:15:34: start X-correlation... INFO @ Sat, 03 Apr 2021 08:15:34: end of X-cor INFO @ Sat, 03 Apr 2021 08:15:34: #2 finished! INFO @ Sat, 03 Apr 2021 08:15:34: #2 predicted fragment length is 97 bps INFO @ Sat, 03 Apr 2021 08:15:34: #2 alternative fragment length(s) may be 3,97,100 bps INFO @ Sat, 03 Apr 2021 08:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.20_model.r WARNING @ Sat, 03 Apr 2021 08:15:34: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:15:34: #2 You may need to consider one of the other alternative d(s): 3,97,100 WARNING @ Sat, 03 Apr 2021 08:15:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:15:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:15:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.10_summits.bed INFO @ Sat, 03 Apr 2021 08:15:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (835 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:15:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277011/SRX7277011.20_summits.bed INFO @ Sat, 03 Apr 2021 08:16:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling