Job ID = 14158310 SRX = SRX10641214 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:33:32 18982754 reads; of these: 18982754 (100.00%) were paired; of these: 11382963 (59.96%) aligned concordantly 0 times 6452048 (33.99%) aligned concordantly exactly 1 time 1147743 (6.05%) aligned concordantly >1 times ---- 11382963 pairs aligned concordantly 0 times; of these: 2996089 (26.32%) aligned discordantly 1 time ---- 8386874 pairs aligned 0 times concordantly or discordantly; of these: 16773748 mates make up the pairs; of these: 15349586 (91.51%) aligned 0 times 786919 (4.69%) aligned exactly 1 time 637243 (3.80%) aligned >1 times 59.57% overall alignment rate Time searching: 00:33:32 Overall time: 00:33:32 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1458170 / 10550594 = 0.1382 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 @ Wed, 08 Dec 2021 16:42:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 16:42:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:42:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:42:37: 1000000 INFO @ Wed, 08 Dec 2021 16:42:47: 2000000 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 @ Wed, 08 Dec 2021 16:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 16:42:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:42:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:42:58: 3000000 INFO @ Wed, 08 Dec 2021 16:43:06: 1000000 INFO @ Wed, 08 Dec 2021 16:43:09: 4000000 INFO @ Wed, 08 Dec 2021 16:43:15: 2000000 INFO @ Wed, 08 Dec 2021 16:43:20: 5000000 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 @ Wed, 08 Dec 2021 16:43:25: 3000000 INFO @ Wed, 08 Dec 2021 16:43:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 16:43:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:43:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:43:31: 6000000 INFO @ Wed, 08 Dec 2021 16:43:35: 4000000 INFO @ Wed, 08 Dec 2021 16:43:38: 1000000 INFO @ Wed, 08 Dec 2021 16:43:42: 7000000 INFO @ Wed, 08 Dec 2021 16:43:45: 5000000 INFO @ Wed, 08 Dec 2021 16:43:49: 2000000 INFO @ Wed, 08 Dec 2021 16:43:53: 8000000 INFO @ Wed, 08 Dec 2021 16:43:55: 6000000 INFO @ Wed, 08 Dec 2021 16:44:00: 3000000 INFO @ Wed, 08 Dec 2021 16:44:04: 9000000 INFO @ Wed, 08 Dec 2021 16:44:05: 7000000 INFO @ Wed, 08 Dec 2021 16:44:11: 4000000 INFO @ Wed, 08 Dec 2021 16:44:15: 8000000 INFO @ Wed, 08 Dec 2021 16:44:16: 10000000 INFO @ Wed, 08 Dec 2021 16:44:22: 5000000 INFO @ Wed, 08 Dec 2021 16:44:25: 9000000 INFO @ Wed, 08 Dec 2021 16:44:27: 11000000 INFO @ Wed, 08 Dec 2021 16:44:34: 6000000 INFO @ Wed, 08 Dec 2021 16:44:36: 10000000 INFO @ Wed, 08 Dec 2021 16:44:39: 12000000 INFO @ Wed, 08 Dec 2021 16:44:46: 7000000 INFO @ Wed, 08 Dec 2021 16:44:47: 11000000 INFO @ Wed, 08 Dec 2021 16:44:50: 13000000 INFO @ Wed, 08 Dec 2021 16:44:57: 8000000 INFO @ Wed, 08 Dec 2021 16:44:57: 12000000 INFO @ Wed, 08 Dec 2021 16:45:01: 14000000 INFO @ Wed, 08 Dec 2021 16:45:07: 13000000 INFO @ Wed, 08 Dec 2021 16:45:08: 9000000 INFO @ Wed, 08 Dec 2021 16:45:12: 15000000 INFO @ Wed, 08 Dec 2021 16:45:16: 14000000 INFO @ Wed, 08 Dec 2021 16:45:19: 10000000 INFO @ Wed, 08 Dec 2021 16:45:23: 16000000 INFO @ Wed, 08 Dec 2021 16:45:26: 15000000 INFO @ Wed, 08 Dec 2021 16:45:30: 11000000 INFO @ Wed, 08 Dec 2021 16:45:34: 17000000 INFO @ Wed, 08 Dec 2021 16:45:35: 16000000 INFO @ Wed, 08 Dec 2021 16:45:40: 12000000 INFO @ Wed, 08 Dec 2021 16:45:45: 17000000 INFO @ Wed, 08 Dec 2021 16:45:45: 18000000 INFO @ Wed, 08 Dec 2021 16:45:51: 13000000 INFO @ Wed, 08 Dec 2021 16:45:54: 18000000 INFO @ Wed, 08 Dec 2021 16:45:56: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:46:02: 14000000 INFO @ Wed, 08 Dec 2021 16:46:04: 19000000 INFO @ Wed, 08 Dec 2021 16:46:04: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:46:04: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:46:04: #1 total tags in treatment: 6475425 INFO @ Wed, 08 Dec 2021 16:46:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:46:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:46:04: #1 tags after filtering in treatment: 5940046 INFO @ Wed, 08 Dec 2021 16:46:04: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:46:04: #1 finished! INFO @ Wed, 08 Dec 2021 16:46:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:46:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:46:05: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 16:46:05: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 16:46:05: start model_add_line... INFO @ Wed, 08 Dec 2021 16:46:05: start X-correlation... INFO @ Wed, 08 Dec 2021 16:46:05: end of X-cor INFO @ Wed, 08 Dec 2021 16:46:05: #2 finished! INFO @ Wed, 08 Dec 2021 16:46:05: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 16:46:05: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 16:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.05_model.r WARNING @ Wed, 08 Dec 2021 16:46:05: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:46:05: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 16:46:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:46:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:46:11: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:46:11: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:46:11: #1 total tags in treatment: 6475425 INFO @ Wed, 08 Dec 2021 16:46:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:46:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:46:11: #1 tags after filtering in treatment: 5940046 INFO @ Wed, 08 Dec 2021 16:46:11: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:46:11: #1 finished! INFO @ Wed, 08 Dec 2021 16:46:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:46:11: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 16:46:11: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 16:46:11: start model_add_line... INFO @ Wed, 08 Dec 2021 16:46:11: start X-correlation... INFO @ Wed, 08 Dec 2021 16:46:11: end of X-cor INFO @ Wed, 08 Dec 2021 16:46:11: #2 finished! INFO @ Wed, 08 Dec 2021 16:46:11: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 16:46:11: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 16:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.10_model.r WARNING @ Wed, 08 Dec 2021 16:46:11: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:46:11: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 16:46:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:46:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:46:13: 15000000 INFO @ Wed, 08 Dec 2021 16:46:24: 16000000 INFO @ Wed, 08 Dec 2021 16:46:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:46:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.05_summits.bed INFO @ Wed, 08 Dec 2021 16:46:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:46:34: 17000000 INFO @ Wed, 08 Dec 2021 16:46:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:46:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:46:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.10_summits.bed INFO @ Wed, 08 Dec 2021 16:46:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:46:45: 18000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:46:56: 19000000 INFO @ Wed, 08 Dec 2021 16:47:03: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:47:03: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:47:03: #1 total tags in treatment: 6475425 INFO @ Wed, 08 Dec 2021 16:47:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:47:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:47:03: #1 tags after filtering in treatment: 5940046 INFO @ Wed, 08 Dec 2021 16:47:03: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:47:03: #1 finished! INFO @ Wed, 08 Dec 2021 16:47:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:47:04: #2 number of paired peaks: 519 WARNING @ Wed, 08 Dec 2021 16:47:04: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Wed, 08 Dec 2021 16:47:04: start model_add_line... INFO @ Wed, 08 Dec 2021 16:47:04: start X-correlation... INFO @ Wed, 08 Dec 2021 16:47:04: end of X-cor INFO @ Wed, 08 Dec 2021 16:47:04: #2 finished! INFO @ Wed, 08 Dec 2021 16:47:04: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 16:47:04: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 16:47:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.20_model.r WARNING @ Wed, 08 Dec 2021 16:47:04: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:47:04: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 16:47:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:47:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:47:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:47:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641214/SRX10641214.20_summits.bed INFO @ Wed, 08 Dec 2021 16:47:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 2 millis CompletedMACS2peakCalling