Job ID = 14158320 SRX = SRX10641217 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: 00:31:22 14718800 reads; of these: 14718800 (100.00%) were paired; of these: 6764513 (45.96%) aligned concordantly 0 times 6719213 (45.65%) aligned concordantly exactly 1 time 1235074 (8.39%) aligned concordantly >1 times ---- 6764513 pairs aligned concordantly 0 times; of these: 1998507 (29.54%) aligned discordantly 1 time ---- 4766006 pairs aligned 0 times concordantly or discordantly; of these: 9532012 mates make up the pairs; of these: 8693949 (91.21%) aligned 0 times 409863 (4.30%) aligned exactly 1 time 428200 (4.49%) aligned >1 times 70.47% overall alignment rate Time searching: 00:31:22 Overall time: 00:31:22 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 16 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] 1135394 / 9915441 = 0.1145 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 16:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.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 16:47:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:47:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:47:39: 1000000 INFO @ Wed, 08 Dec 2021 16:47:50: 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 16:47:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.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 16:47:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:47:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:48:02: 3000000 INFO @ Wed, 08 Dec 2021 16:48:10: 1000000 INFO @ Wed, 08 Dec 2021 16:48:13: 4000000 INFO @ Wed, 08 Dec 2021 16:48:22: 2000000 INFO @ Wed, 08 Dec 2021 16:48:24: 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 16:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.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 16:48:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:48:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:48:34: 3000000 INFO @ Wed, 08 Dec 2021 16:48:35: 6000000 INFO @ Wed, 08 Dec 2021 16:48:43: 1000000 INFO @ Wed, 08 Dec 2021 16:48:46: 4000000 INFO @ Wed, 08 Dec 2021 16:48:47: 7000000 INFO @ Wed, 08 Dec 2021 16:48:56: 2000000 INFO @ Wed, 08 Dec 2021 16:48:58: 5000000 INFO @ Wed, 08 Dec 2021 16:48:59: 8000000 INFO @ Wed, 08 Dec 2021 16:49:10: 3000000 INFO @ Wed, 08 Dec 2021 16:49:10: 6000000 INFO @ Wed, 08 Dec 2021 16:49:11: 9000000 INFO @ Wed, 08 Dec 2021 16:49:22: 7000000 INFO @ Wed, 08 Dec 2021 16:49:23: 10000000 INFO @ Wed, 08 Dec 2021 16:49:23: 4000000 INFO @ Wed, 08 Dec 2021 16:49:34: 8000000 INFO @ Wed, 08 Dec 2021 16:49:35: 11000000 INFO @ Wed, 08 Dec 2021 16:49:37: 5000000 INFO @ Wed, 08 Dec 2021 16:49:47: 9000000 INFO @ Wed, 08 Dec 2021 16:49:47: 12000000 INFO @ Wed, 08 Dec 2021 16:49:51: 6000000 INFO @ Wed, 08 Dec 2021 16:49:59: 10000000 INFO @ Wed, 08 Dec 2021 16:50:00: 13000000 INFO @ Wed, 08 Dec 2021 16:50:05: 7000000 INFO @ Wed, 08 Dec 2021 16:50:12: 11000000 INFO @ Wed, 08 Dec 2021 16:50:12: 14000000 INFO @ Wed, 08 Dec 2021 16:50:20: 8000000 INFO @ Wed, 08 Dec 2021 16:50:24: 12000000 INFO @ Wed, 08 Dec 2021 16:50:25: 15000000 INFO @ Wed, 08 Dec 2021 16:50:35: 9000000 INFO @ Wed, 08 Dec 2021 16:50:37: 13000000 INFO @ Wed, 08 Dec 2021 16:50:37: 16000000 INFO @ Wed, 08 Dec 2021 16:50:49: 14000000 INFO @ Wed, 08 Dec 2021 16:50:49: 17000000 INFO @ Wed, 08 Dec 2021 16:50:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:51:01: 18000000 INFO @ Wed, 08 Dec 2021 16:51:01: 15000000 INFO @ Wed, 08 Dec 2021 16:51:04: 11000000 INFO @ Wed, 08 Dec 2021 16:51:07: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:51:07: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:51:07: #1 total tags in treatment: 6996820 INFO @ Wed, 08 Dec 2021 16:51:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:51:07: #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 16:51:07: #1 tags after filtering in treatment: 6535300 INFO @ Wed, 08 Dec 2021 16:51:07: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:51:07: #1 finished! INFO @ Wed, 08 Dec 2021 16:51:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:51:07: #2 number of paired peaks: 531 WARNING @ Wed, 08 Dec 2021 16:51:07: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Wed, 08 Dec 2021 16:51:07: start model_add_line... INFO @ Wed, 08 Dec 2021 16:51:08: start X-correlation... INFO @ Wed, 08 Dec 2021 16:51:08: end of X-cor INFO @ Wed, 08 Dec 2021 16:51:08: #2 finished! INFO @ Wed, 08 Dec 2021 16:51:08: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 16:51:08: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 16:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.05_model.r WARNING @ Wed, 08 Dec 2021 16:51:08: #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 16:51:08: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 16:51:08: #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 16:51:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:51:13: 16000000 INFO @ Wed, 08 Dec 2021 16:51:18: 12000000 INFO @ Wed, 08 Dec 2021 16:51:24: 17000000 INFO @ Wed, 08 Dec 2021 16:51:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:51:32: 13000000 INFO @ Wed, 08 Dec 2021 16:51:36: 18000000 INFO @ Wed, 08 Dec 2021 16:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.05_summits.bed INFO @ Wed, 08 Dec 2021 16:51:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:51:41: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:51:41: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:51:41: #1 total tags in treatment: 6996820 INFO @ Wed, 08 Dec 2021 16:51:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:51:41: #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 16:51:41: #1 tags after filtering in treatment: 6535300 INFO @ Wed, 08 Dec 2021 16:51:41: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:51:41: #1 finished! INFO @ Wed, 08 Dec 2021 16:51:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:51:42: #2 number of paired peaks: 531 WARNING @ Wed, 08 Dec 2021 16:51:42: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Wed, 08 Dec 2021 16:51:42: start model_add_line... INFO @ Wed, 08 Dec 2021 16:51:42: start X-correlation... INFO @ Wed, 08 Dec 2021 16:51:42: end of X-cor INFO @ Wed, 08 Dec 2021 16:51:42: #2 finished! INFO @ Wed, 08 Dec 2021 16:51:42: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 16:51:42: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 16:51:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.10_model.r WARNING @ Wed, 08 Dec 2021 16:51:42: #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 16:51:42: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 16:51:42: #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 16:51:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:51:46: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:52:00: 15000000 INFO @ Wed, 08 Dec 2021 16:52:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.10_summits.bed INFO @ Wed, 08 Dec 2021 16:52:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:52:13: 16000000 INFO @ Wed, 08 Dec 2021 16:52:27: 17000000 INFO @ Wed, 08 Dec 2021 16:52:41: 18000000 INFO @ Wed, 08 Dec 2021 16:52:47: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:52:47: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:52:47: #1 total tags in treatment: 6996820 INFO @ Wed, 08 Dec 2021 16:52:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:52:47: #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 16:52:47: #1 tags after filtering in treatment: 6535300 INFO @ Wed, 08 Dec 2021 16:52:47: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:52:47: #1 finished! INFO @ Wed, 08 Dec 2021 16:52:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:52:48: #2 number of paired peaks: 531 WARNING @ Wed, 08 Dec 2021 16:52:48: Fewer paired peaks (531) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 531 pairs to build model! INFO @ Wed, 08 Dec 2021 16:52:48: start model_add_line... INFO @ Wed, 08 Dec 2021 16:52:48: start X-correlation... INFO @ Wed, 08 Dec 2021 16:52:48: end of X-cor INFO @ Wed, 08 Dec 2021 16:52:48: #2 finished! INFO @ Wed, 08 Dec 2021 16:52:48: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 16:52:48: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 16:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.20_model.r WARNING @ Wed, 08 Dec 2021 16:52:48: #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 16:52:48: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 16:52:48: #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 16:52:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:53:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:53:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641217/SRX10641217.20_summits.bed INFO @ Wed, 08 Dec 2021 16:53:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 8 millis CompletedMACS2peakCalling