Job ID = 14159948 SRX = SRX8845648 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: 00:40:35 25233363 reads; of these: 25233363 (100.00%) were paired; of these: 10336649 (40.96%) aligned concordantly 0 times 13014009 (51.57%) aligned concordantly exactly 1 time 1882705 (7.46%) aligned concordantly >1 times ---- 10336649 pairs aligned concordantly 0 times; of these: 2297381 (22.23%) aligned discordantly 1 time ---- 8039268 pairs aligned 0 times concordantly or discordantly; of these: 16078536 mates make up the pairs; of these: 15009344 (93.35%) aligned 0 times 350582 (2.18%) aligned exactly 1 time 718610 (4.47%) aligned >1 times 70.26% overall alignment rate Time searching: 00:40:35 Overall time: 00:40:35 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 24 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] 4258393 / 17113158 = 0.2488 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 @ Thu, 09 Dec 2021 01:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.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 @ Thu, 09 Dec 2021 01:36:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:36:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:36:50: 1000000 INFO @ Thu, 09 Dec 2021 01:37:00: 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 @ Thu, 09 Dec 2021 01:37:10: 3000000 INFO @ Thu, 09 Dec 2021 01:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.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 @ Thu, 09 Dec 2021 01:37:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:37:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:37:21: 1000000 INFO @ Thu, 09 Dec 2021 01:37:22: 4000000 INFO @ Thu, 09 Dec 2021 01:37:34: 2000000 INFO @ Thu, 09 Dec 2021 01:37:34: 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 @ Thu, 09 Dec 2021 01:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.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 @ Thu, 09 Dec 2021 01:37:41: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:37:41: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:37:46: 6000000 INFO @ Thu, 09 Dec 2021 01:37:46: 3000000 INFO @ Thu, 09 Dec 2021 01:37:53: 1000000 INFO @ Thu, 09 Dec 2021 01:37:56: 7000000 INFO @ Thu, 09 Dec 2021 01:37:56: 4000000 INFO @ Thu, 09 Dec 2021 01:38:03: 2000000 INFO @ Thu, 09 Dec 2021 01:38:07: 8000000 INFO @ Thu, 09 Dec 2021 01:38:07: 5000000 INFO @ Thu, 09 Dec 2021 01:38:14: 3000000 INFO @ Thu, 09 Dec 2021 01:38:17: 6000000 INFO @ Thu, 09 Dec 2021 01:38:17: 9000000 INFO @ Thu, 09 Dec 2021 01:38:24: 4000000 INFO @ Thu, 09 Dec 2021 01:38:27: 7000000 INFO @ Thu, 09 Dec 2021 01:38:28: 10000000 INFO @ Thu, 09 Dec 2021 01:38:35: 5000000 INFO @ Thu, 09 Dec 2021 01:38:38: 8000000 INFO @ Thu, 09 Dec 2021 01:38:38: 11000000 INFO @ Thu, 09 Dec 2021 01:38:46: 6000000 INFO @ Thu, 09 Dec 2021 01:38:48: 9000000 INFO @ Thu, 09 Dec 2021 01:38:49: 12000000 INFO @ Thu, 09 Dec 2021 01:38:57: 7000000 INFO @ Thu, 09 Dec 2021 01:38:59: 13000000 INFO @ Thu, 09 Dec 2021 01:39:00: 10000000 INFO @ Thu, 09 Dec 2021 01:39:09: 14000000 INFO @ Thu, 09 Dec 2021 01:39:09: 8000000 INFO @ Thu, 09 Dec 2021 01:39:10: 11000000 INFO @ Thu, 09 Dec 2021 01:39:19: 15000000 INFO @ Thu, 09 Dec 2021 01:39:20: 12000000 INFO @ Thu, 09 Dec 2021 01:39:22: 9000000 INFO @ Thu, 09 Dec 2021 01:39:30: 16000000 INFO @ Thu, 09 Dec 2021 01:39:31: 13000000 INFO @ Thu, 09 Dec 2021 01:39:34: 10000000 INFO @ Thu, 09 Dec 2021 01:39:42: 14000000 INFO @ Thu, 09 Dec 2021 01:39:42: 17000000 INFO @ Thu, 09 Dec 2021 01:39:45: 11000000 INFO @ Thu, 09 Dec 2021 01:39:53: 15000000 INFO @ Thu, 09 Dec 2021 01:39:53: 18000000 INFO @ Thu, 09 Dec 2021 01:39:56: 12000000 INFO @ Thu, 09 Dec 2021 01:40:04: 16000000 INFO @ Thu, 09 Dec 2021 01:40:05: 19000000 INFO @ Thu, 09 Dec 2021 01:40:08: 13000000 INFO @ Thu, 09 Dec 2021 01:40:15: 17000000 INFO @ Thu, 09 Dec 2021 01:40:16: 20000000 INFO @ Thu, 09 Dec 2021 01:40:19: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:40:26: 18000000 INFO @ Thu, 09 Dec 2021 01:40:28: 21000000 INFO @ Thu, 09 Dec 2021 01:40:31: 15000000 INFO @ Thu, 09 Dec 2021 01:40:38: 19000000 INFO @ Thu, 09 Dec 2021 01:40:39: 22000000 INFO @ Thu, 09 Dec 2021 01:40:42: 16000000 INFO @ Thu, 09 Dec 2021 01:40:49: 20000000 INFO @ Thu, 09 Dec 2021 01:40:50: 23000000 INFO @ Thu, 09 Dec 2021 01:40:53: 17000000 INFO @ Thu, 09 Dec 2021 01:41:01: 21000000 INFO @ Thu, 09 Dec 2021 01:41:02: 24000000 INFO @ Thu, 09 Dec 2021 01:41:05: 18000000 INFO @ Thu, 09 Dec 2021 01:41:12: 22000000 INFO @ Thu, 09 Dec 2021 01:41:14: 25000000 INFO @ Thu, 09 Dec 2021 01:41:16: 19000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:41:24: 23000000 INFO @ Thu, 09 Dec 2021 01:41:27: 20000000 INFO @ Thu, 09 Dec 2021 01:41:27: 26000000 INFO @ Thu, 09 Dec 2021 01:41:35: 24000000 INFO @ Thu, 09 Dec 2021 01:41:38: 21000000 INFO @ Thu, 09 Dec 2021 01:41:38: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:41:38: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:41:38: #1 total tags in treatment: 11214714 INFO @ Thu, 09 Dec 2021 01:41:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:41:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:41:38: #1 tags after filtering in treatment: 8190712 INFO @ Thu, 09 Dec 2021 01:41:38: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 01:41:38: #1 finished! INFO @ Thu, 09 Dec 2021 01:41:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:41:39: #2 number of paired peaks: 735 WARNING @ Thu, 09 Dec 2021 01:41:39: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Thu, 09 Dec 2021 01:41:39: start model_add_line... INFO @ Thu, 09 Dec 2021 01:41:39: start X-correlation... INFO @ Thu, 09 Dec 2021 01:41:39: end of X-cor INFO @ Thu, 09 Dec 2021 01:41:39: #2 finished! INFO @ Thu, 09 Dec 2021 01:41:39: #2 predicted fragment length is 209 bps INFO @ Thu, 09 Dec 2021 01:41:39: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 09 Dec 2021 01:41:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.05_model.r WARNING @ Thu, 09 Dec 2021 01:41:39: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:41:39: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Thu, 09 Dec 2021 01:41:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:41:39: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:41:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:41:47: 25000000 INFO @ Thu, 09 Dec 2021 01:41:49: 22000000 INFO @ Thu, 09 Dec 2021 01:41:59: 26000000 INFO @ Thu, 09 Dec 2021 01:41:59: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:42:00: 23000000 INFO @ Thu, 09 Dec 2021 01:42:10: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:42:10: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:42:10: #1 total tags in treatment: 11214714 INFO @ Thu, 09 Dec 2021 01:42:10: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:42:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:42:10: #1 tags after filtering in treatment: 8190712 INFO @ Thu, 09 Dec 2021 01:42:10: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 01:42:10: #1 finished! INFO @ Thu, 09 Dec 2021 01:42:10: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:42:11: #2 number of paired peaks: 735 WARNING @ Thu, 09 Dec 2021 01:42:11: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Thu, 09 Dec 2021 01:42:11: start model_add_line... INFO @ Thu, 09 Dec 2021 01:42:11: start X-correlation... INFO @ Thu, 09 Dec 2021 01:42:11: end of X-cor INFO @ Thu, 09 Dec 2021 01:42:11: #2 finished! INFO @ Thu, 09 Dec 2021 01:42:11: #2 predicted fragment length is 209 bps INFO @ Thu, 09 Dec 2021 01:42:11: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 09 Dec 2021 01:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.10_model.r WARNING @ Thu, 09 Dec 2021 01:42:11: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:42:11: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Thu, 09 Dec 2021 01:42:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:42:11: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.05_summits.bed INFO @ Thu, 09 Dec 2021 01:42:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5926 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:42:11: 24000000 INFO @ Thu, 09 Dec 2021 01:42:23: 25000000 INFO @ Thu, 09 Dec 2021 01:42:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:42:35: 26000000 INFO @ Thu, 09 Dec 2021 01:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.10_summits.bed INFO @ Thu, 09 Dec 2021 01:42:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3430 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:42:47: #1 tag size is determined as 125 bps INFO @ Thu, 09 Dec 2021 01:42:47: #1 tag size = 125 INFO @ Thu, 09 Dec 2021 01:42:47: #1 total tags in treatment: 11214714 INFO @ Thu, 09 Dec 2021 01:42:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:42:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:42:47: #1 tags after filtering in treatment: 8190712 INFO @ Thu, 09 Dec 2021 01:42:47: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 01:42:47: #1 finished! INFO @ Thu, 09 Dec 2021 01:42:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:42:48: #2 number of paired peaks: 735 WARNING @ Thu, 09 Dec 2021 01:42:48: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Thu, 09 Dec 2021 01:42:48: start model_add_line... INFO @ Thu, 09 Dec 2021 01:42:48: start X-correlation... INFO @ Thu, 09 Dec 2021 01:42:48: end of X-cor INFO @ Thu, 09 Dec 2021 01:42:48: #2 finished! INFO @ Thu, 09 Dec 2021 01:42:48: #2 predicted fragment length is 209 bps INFO @ Thu, 09 Dec 2021 01:42:48: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 09 Dec 2021 01:42:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.20_model.r WARNING @ Thu, 09 Dec 2021 01:42:48: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:42:48: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Thu, 09 Dec 2021 01:42:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:42:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:42:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:43:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845648/SRX8845648.20_summits.bed INFO @ Thu, 09 Dec 2021 01:43:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1482 records, 4 fields): 3 millis CompletedMACS2peakCalling