Job ID = 14170585 SRX = SRX8497043 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12472271 spots for SRR11952642/SRR11952642.sra Written 12472271 spots for SRR11952642/SRR11952642.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171071 ("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: 00:28:26 12472271 reads; of these: 12472271 (100.00%) were paired; of these: 1764896 (14.15%) aligned concordantly 0 times 7992809 (64.08%) aligned concordantly exactly 1 time 2714566 (21.76%) aligned concordantly >1 times ---- 1764896 pairs aligned concordantly 0 times; of these: 608840 (34.50%) aligned discordantly 1 time ---- 1156056 pairs aligned 0 times concordantly or discordantly; of these: 2312112 mates make up the pairs; of these: 1650160 (71.37%) aligned 0 times 231480 (10.01%) aligned exactly 1 time 430472 (18.62%) aligned >1 times 93.38% overall alignment rate Time searching: 00:28:26 Overall time: 00:28:26 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] 429881 / 11257674 = 0.0382 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 07:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.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 07:57:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:57:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:57:45: 1000000 INFO @ Sat, 11 Dec 2021 07:57:51: 2000000 INFO @ Sat, 11 Dec 2021 07:57:57: 3000000 INFO @ Sat, 11 Dec 2021 07:58:02: 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 07:58:08: 5000000 INFO @ Sat, 11 Dec 2021 07:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.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 07:58:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:16: 6000000 INFO @ Sat, 11 Dec 2021 07:58:17: 1000000 INFO @ Sat, 11 Dec 2021 07:58:23: 7000000 INFO @ Sat, 11 Dec 2021 07:58:25: 2000000 INFO @ Sat, 11 Dec 2021 07:58:30: 8000000 INFO @ Sat, 11 Dec 2021 07:58:33: 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 @ Sat, 11 Dec 2021 07:58:38: 9000000 INFO @ Sat, 11 Dec 2021 07:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.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 07:58:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:41: 4000000 INFO @ Sat, 11 Dec 2021 07:58:45: 10000000 INFO @ Sat, 11 Dec 2021 07:58:46: 1000000 INFO @ Sat, 11 Dec 2021 07:58:50: 5000000 INFO @ Sat, 11 Dec 2021 07:58:53: 11000000 INFO @ Sat, 11 Dec 2021 07:58:54: 2000000 INFO @ Sat, 11 Dec 2021 07:58:58: 6000000 INFO @ Sat, 11 Dec 2021 07:59:01: 12000000 INFO @ Sat, 11 Dec 2021 07:59:01: 3000000 INFO @ Sat, 11 Dec 2021 07:59:06: 7000000 INFO @ Sat, 11 Dec 2021 07:59:08: 13000000 INFO @ Sat, 11 Dec 2021 07:59:09: 4000000 INFO @ Sat, 11 Dec 2021 07:59:15: 8000000 INFO @ Sat, 11 Dec 2021 07:59:16: 14000000 INFO @ Sat, 11 Dec 2021 07:59:17: 5000000 INFO @ Sat, 11 Dec 2021 07:59:23: 9000000 INFO @ Sat, 11 Dec 2021 07:59:23: 15000000 INFO @ Sat, 11 Dec 2021 07:59:24: 6000000 INFO @ Sat, 11 Dec 2021 07:59:31: 16000000 INFO @ Sat, 11 Dec 2021 07:59:32: 10000000 INFO @ Sat, 11 Dec 2021 07:59:32: 7000000 INFO @ Sat, 11 Dec 2021 07:59:39: 17000000 INFO @ Sat, 11 Dec 2021 07:59:39: 8000000 INFO @ Sat, 11 Dec 2021 07:59:40: 11000000 INFO @ Sat, 11 Dec 2021 07:59:46: 18000000 INFO @ Sat, 11 Dec 2021 07:59:47: 9000000 INFO @ Sat, 11 Dec 2021 07:59:48: 12000000 INFO @ Sat, 11 Dec 2021 07:59:54: 19000000 INFO @ Sat, 11 Dec 2021 07:59:55: 10000000 INFO @ Sat, 11 Dec 2021 07:59:57: 13000000 INFO @ Sat, 11 Dec 2021 08:00:02: 20000000 INFO @ Sat, 11 Dec 2021 08:00:02: 11000000 INFO @ Sat, 11 Dec 2021 08:00:05: 14000000 INFO @ Sat, 11 Dec 2021 08:00:09: 21000000 INFO @ Sat, 11 Dec 2021 08:00:10: 12000000 INFO @ Sat, 11 Dec 2021 08:00:13: 15000000 INFO @ Sat, 11 Dec 2021 08:00:17: 22000000 INFO @ Sat, 11 Dec 2021 08:00:17: 13000000 INFO @ Sat, 11 Dec 2021 08:00:20: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:00:20: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:00:20: #1 total tags in treatment: 10292237 INFO @ Sat, 11 Dec 2021 08:00:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:00:20: #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 08:00:20: #1 tags after filtering in treatment: 9913335 INFO @ Sat, 11 Dec 2021 08:00:20: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 08:00:20: #1 finished! INFO @ Sat, 11 Dec 2021 08:00:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:00:21: #2 number of paired peaks: 113 WARNING @ Sat, 11 Dec 2021 08:00:21: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 11 Dec 2021 08:00:21: start model_add_line... INFO @ Sat, 11 Dec 2021 08:00:21: start X-correlation... INFO @ Sat, 11 Dec 2021 08:00:21: end of X-cor INFO @ Sat, 11 Dec 2021 08:00:21: #2 finished! INFO @ Sat, 11 Dec 2021 08:00:21: #2 predicted fragment length is 160 bps INFO @ Sat, 11 Dec 2021 08:00:21: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 11 Dec 2021 08:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.05_model.r WARNING @ Sat, 11 Dec 2021 08:00:21: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:00:21: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 11 Dec 2021 08:00:21: #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 08:00:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:00:22: 16000000 INFO @ Sat, 11 Dec 2021 08:00:25: 14000000 INFO @ Sat, 11 Dec 2021 08:00:30: 17000000 INFO @ Sat, 11 Dec 2021 08:00:32: 15000000 INFO @ Sat, 11 Dec 2021 08:00:39: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:00:40: 16000000 INFO @ Sat, 11 Dec 2021 08:00:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:00:47: 17000000 INFO @ Sat, 11 Dec 2021 08:00:47: 19000000 INFO @ Sat, 11 Dec 2021 08:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.05_summits.bed INFO @ Sat, 11 Dec 2021 08:00:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1306 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:00:54: 18000000 INFO @ Sat, 11 Dec 2021 08:00:55: 20000000 INFO @ Sat, 11 Dec 2021 08:01:02: 19000000 INFO @ Sat, 11 Dec 2021 08:01:04: 21000000 INFO @ Sat, 11 Dec 2021 08:01:09: 20000000 INFO @ Sat, 11 Dec 2021 08:01:12: 22000000 INFO @ Sat, 11 Dec 2021 08:01:16: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:01:16: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:01:16: #1 total tags in treatment: 10292237 INFO @ Sat, 11 Dec 2021 08:01:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:16: #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 08:01:16: #1 tags after filtering in treatment: 9913335 INFO @ Sat, 11 Dec 2021 08:01:16: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 08:01:16: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:17: 21000000 INFO @ Sat, 11 Dec 2021 08:01:17: #2 number of paired peaks: 113 WARNING @ Sat, 11 Dec 2021 08:01:17: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 11 Dec 2021 08:01:17: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:17: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:17: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:17: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:17: #2 predicted fragment length is 160 bps INFO @ Sat, 11 Dec 2021 08:01:17: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 11 Dec 2021 08:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.10_model.r WARNING @ Sat, 11 Dec 2021 08:01:17: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:17: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 11 Dec 2021 08:01:17: #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 08:01:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:23: 22000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:01:26: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 08:01:26: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 08:01:26: #1 total tags in treatment: 10292237 INFO @ Sat, 11 Dec 2021 08:01:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:26: #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 08:01:27: #1 tags after filtering in treatment: 9913335 INFO @ Sat, 11 Dec 2021 08:01:27: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 08:01:27: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:27: #2 number of paired peaks: 113 WARNING @ Sat, 11 Dec 2021 08:01:27: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 11 Dec 2021 08:01:27: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:27: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:27: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:27: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:27: #2 predicted fragment length is 160 bps INFO @ Sat, 11 Dec 2021 08:01:27: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 11 Dec 2021 08:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.20_model.r WARNING @ Sat, 11 Dec 2021 08:01:27: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:27: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 11 Dec 2021 08:01:27: #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 08:01:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:01:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:01:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.10_summits.bed INFO @ Sat, 11 Dec 2021 08:01:46: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (688 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:01:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8497043/SRX8497043.20_summits.bed INFO @ Sat, 11 Dec 2021 08:01:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 millis CompletedMACS2peakCalling