Job ID = 16435529 SRX = SRX13336896 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: 00:41:23 36102593 reads; of these: 36102593 (100.00%) were paired; of these: 26710355 (73.98%) aligned concordantly 0 times 8075499 (22.37%) aligned concordantly exactly 1 time 1316739 (3.65%) aligned concordantly >1 times ---- 26710355 pairs aligned concordantly 0 times; of these: 8055468 (30.16%) aligned discordantly 1 time ---- 18654887 pairs aligned 0 times concordantly or discordantly; of these: 37309774 mates make up the pairs; of these: 33736903 (90.42%) aligned 0 times 2076483 (5.57%) aligned exactly 1 time 1496388 (4.01%) aligned >1 times 53.28% overall alignment rate Time searching: 00:41:23 Overall time: 00:41:23 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 28 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] 1926480 / 17420838 = 0.1106 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.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 @ Tue, 02 Aug 2022 11:46:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:46:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:46:38: 1000000 INFO @ Tue, 02 Aug 2022 11:46:47: 2000000 INFO @ Tue, 02 Aug 2022 11:46:56: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.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 @ Tue, 02 Aug 2022 11:47:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:05: 4000000 INFO @ Tue, 02 Aug 2022 11:47:08: 1000000 INFO @ Tue, 02 Aug 2022 11:47:15: 5000000 INFO @ Tue, 02 Aug 2022 11:47:17: 2000000 INFO @ Tue, 02 Aug 2022 11:47:24: 6000000 INFO @ Tue, 02 Aug 2022 11:47:25: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.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 @ Tue, 02 Aug 2022 11:47:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:34: 4000000 INFO @ Tue, 02 Aug 2022 11:47:35: 7000000 INFO @ Tue, 02 Aug 2022 11:47:38: 1000000 INFO @ Tue, 02 Aug 2022 11:47:42: 5000000 INFO @ Tue, 02 Aug 2022 11:47:45: 8000000 INFO @ Tue, 02 Aug 2022 11:47:46: 2000000 INFO @ Tue, 02 Aug 2022 11:47:51: 6000000 INFO @ Tue, 02 Aug 2022 11:47:55: 3000000 INFO @ Tue, 02 Aug 2022 11:47:55: 9000000 INFO @ Tue, 02 Aug 2022 11:48:00: 7000000 INFO @ Tue, 02 Aug 2022 11:48:04: 4000000 INFO @ Tue, 02 Aug 2022 11:48:05: 10000000 INFO @ Tue, 02 Aug 2022 11:48:10: 8000000 INFO @ Tue, 02 Aug 2022 11:48:12: 5000000 INFO @ Tue, 02 Aug 2022 11:48:15: 11000000 INFO @ Tue, 02 Aug 2022 11:48:18: 9000000 INFO @ Tue, 02 Aug 2022 11:48:21: 6000000 INFO @ Tue, 02 Aug 2022 11:48:26: 12000000 INFO @ Tue, 02 Aug 2022 11:48:27: 10000000 INFO @ Tue, 02 Aug 2022 11:48:30: 7000000 INFO @ Tue, 02 Aug 2022 11:48:36: 11000000 INFO @ Tue, 02 Aug 2022 11:48:36: 13000000 INFO @ Tue, 02 Aug 2022 11:48:39: 8000000 INFO @ Tue, 02 Aug 2022 11:48:45: 12000000 INFO @ Tue, 02 Aug 2022 11:48:46: 14000000 INFO @ Tue, 02 Aug 2022 11:48:48: 9000000 INFO @ Tue, 02 Aug 2022 11:48:54: 13000000 INFO @ Tue, 02 Aug 2022 11:48:56: 15000000 INFO @ Tue, 02 Aug 2022 11:48:57: 10000000 INFO @ Tue, 02 Aug 2022 11:49:03: 14000000 INFO @ Tue, 02 Aug 2022 11:49:05: 16000000 INFO @ Tue, 02 Aug 2022 11:49:06: 11000000 INFO @ Tue, 02 Aug 2022 11:49:12: 15000000 INFO @ Tue, 02 Aug 2022 11:49:15: 17000000 INFO @ Tue, 02 Aug 2022 11:49:15: 12000000 INFO @ Tue, 02 Aug 2022 11:49:21: 16000000 INFO @ Tue, 02 Aug 2022 11:49:24: 13000000 INFO @ Tue, 02 Aug 2022 11:49:24: 18000000 INFO @ Tue, 02 Aug 2022 11:49:31: 17000000 INFO @ Tue, 02 Aug 2022 11:49:33: 14000000 INFO @ Tue, 02 Aug 2022 11:49:34: 19000000 INFO @ Tue, 02 Aug 2022 11:49:40: 18000000 INFO @ Tue, 02 Aug 2022 11:49:42: 15000000 INFO @ Tue, 02 Aug 2022 11:49:43: 20000000 INFO @ Tue, 02 Aug 2022 11:49:49: 19000000 INFO @ Tue, 02 Aug 2022 11:49:51: 16000000 INFO @ Tue, 02 Aug 2022 11:49:53: 21000000 INFO @ Tue, 02 Aug 2022 11:49:58: 20000000 INFO @ Tue, 02 Aug 2022 11:50:00: 17000000 INFO @ Tue, 02 Aug 2022 11:50:02: 22000000 INFO @ Tue, 02 Aug 2022 11:50:07: 21000000 INFO @ Tue, 02 Aug 2022 11:50:09: 18000000 INFO @ Tue, 02 Aug 2022 11:50:12: 23000000 INFO @ Tue, 02 Aug 2022 11:50:17: 22000000 INFO @ Tue, 02 Aug 2022 11:50:19: 19000000 INFO @ Tue, 02 Aug 2022 11:50:21: 24000000 INFO @ Tue, 02 Aug 2022 11:50:26: 23000000 INFO @ Tue, 02 Aug 2022 11:50:28: 20000000 INFO @ Tue, 02 Aug 2022 11:50:31: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:50:35: 24000000 INFO @ Tue, 02 Aug 2022 11:50:37: 21000000 INFO @ Tue, 02 Aug 2022 11:50:40: 26000000 INFO @ Tue, 02 Aug 2022 11:50:44: 25000000 INFO @ Tue, 02 Aug 2022 11:50:46: 22000000 INFO @ Tue, 02 Aug 2022 11:50:50: 27000000 INFO @ Tue, 02 Aug 2022 11:50:53: 26000000 INFO @ Tue, 02 Aug 2022 11:50:55: 23000000 INFO @ Tue, 02 Aug 2022 11:50:59: 28000000 INFO @ Tue, 02 Aug 2022 11:51:03: 27000000 INFO @ Tue, 02 Aug 2022 11:51:05: 24000000 INFO @ Tue, 02 Aug 2022 11:51:09: 29000000 INFO @ Tue, 02 Aug 2022 11:51:12: 28000000 INFO @ Tue, 02 Aug 2022 11:51:14: 25000000 INFO @ Tue, 02 Aug 2022 11:51:19: 30000000 INFO @ Tue, 02 Aug 2022 11:51:21: 29000000 INFO @ Tue, 02 Aug 2022 11:51:23: 26000000 INFO @ Tue, 02 Aug 2022 11:51:28: 31000000 INFO @ Tue, 02 Aug 2022 11:51:30: 30000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:51:32: 27000000 INFO @ Tue, 02 Aug 2022 11:51:37: 32000000 INFO @ Tue, 02 Aug 2022 11:51:40: 31000000 INFO @ Tue, 02 Aug 2022 11:51:42: 28000000 INFO @ Tue, 02 Aug 2022 11:51:47: 33000000 INFO @ Tue, 02 Aug 2022 11:51:50: 32000000 INFO @ Tue, 02 Aug 2022 11:51:51: 29000000 INFO @ Tue, 02 Aug 2022 11:51:56: 34000000 INFO @ Tue, 02 Aug 2022 11:52:00: 33000000 INFO @ Tue, 02 Aug 2022 11:52:01: 30000000 INFO @ Tue, 02 Aug 2022 11:52:03: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:52:03: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:52:03: #1 total tags in treatment: 8203518 INFO @ Tue, 02 Aug 2022 11:52:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:03: #1 tags after filtering in treatment: 7688534 INFO @ Tue, 02 Aug 2022 11:52:03: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 11:52:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:03: #2 number of paired peaks: 486 WARNING @ Tue, 02 Aug 2022 11:52:03: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 02 Aug 2022 11:52:03: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:03: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:03: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:03: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:03: #2 predicted fragment length is 230 bps INFO @ Tue, 02 Aug 2022 11:52:03: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 02 Aug 2022 11:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.05_model.r WARNING @ Tue, 02 Aug 2022 11:52:03: #2 Since the d (230) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:03: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Tue, 02 Aug 2022 11:52:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:52:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:10: 34000000 INFO @ Tue, 02 Aug 2022 11:52:11: 31000000 INFO @ Tue, 02 Aug 2022 11:52:16: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:52:16: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:52:16: #1 total tags in treatment: 8203518 INFO @ Tue, 02 Aug 2022 11:52:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:16: #1 tags after filtering in treatment: 7688534 INFO @ Tue, 02 Aug 2022 11:52:16: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 11:52:16: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:17: #2 number of paired peaks: 486 WARNING @ Tue, 02 Aug 2022 11:52:17: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 02 Aug 2022 11:52:17: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:17: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:17: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:17: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:17: #2 predicted fragment length is 230 bps INFO @ Tue, 02 Aug 2022 11:52:17: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 02 Aug 2022 11:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.10_model.r WARNING @ Tue, 02 Aug 2022 11:52:17: #2 Since the d (230) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:17: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Tue, 02 Aug 2022 11:52:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:52:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:21: 32000000 INFO @ Tue, 02 Aug 2022 11:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.05_summits.bed INFO @ Tue, 02 Aug 2022 11:52:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:52:29: 33000000 INFO @ Tue, 02 Aug 2022 11:52:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:38: 34000000 INFO @ Tue, 02 Aug 2022 11:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.10_summits.bed INFO @ Tue, 02 Aug 2022 11:52:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:52:43: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:52:43: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:52:43: #1 total tags in treatment: 8203518 INFO @ Tue, 02 Aug 2022 11:52:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:43: #1 tags after filtering in treatment: 7688534 INFO @ Tue, 02 Aug 2022 11:52:43: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 11:52:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:44: #2 number of paired peaks: 486 WARNING @ Tue, 02 Aug 2022 11:52:44: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 02 Aug 2022 11:52:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:44: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:44: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:44: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:44: #2 predicted fragment length is 230 bps INFO @ Tue, 02 Aug 2022 11:52:44: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 02 Aug 2022 11:52:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.20_model.r WARNING @ Tue, 02 Aug 2022 11:52:44: #2 Since the d (230) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:44: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Tue, 02 Aug 2022 11:52:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:52:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336896/SRX13336896.20_summits.bed INFO @ Tue, 02 Aug 2022 11:53:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 266 millis CompletedMACS2peakCalling