Job ID = 16435034 SRX = SRX13336908 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: 00:00:01 Multiseed full-index search: 00:52:05 22465377 reads; of these: 22465377 (100.00%) were paired; of these: 13268015 (59.06%) aligned concordantly 0 times 7657971 (34.09%) aligned concordantly exactly 1 time 1539391 (6.85%) aligned concordantly >1 times ---- 13268015 pairs aligned concordantly 0 times; of these: 5711906 (43.05%) aligned discordantly 1 time ---- 7556109 pairs aligned 0 times concordantly or discordantly; of these: 15112218 mates make up the pairs; of these: 12681650 (83.92%) aligned 0 times 1240855 (8.21%) aligned exactly 1 time 1189713 (7.87%) aligned >1 times 71.78% overall alignment rate Time searching: 00:52:07 Overall time: 00:52:07 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] 1248020 / 14876131 = 0.0839 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 11:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.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 11:48:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:49:03: 1000000 INFO @ Tue, 02 Aug 2022 11:49:13: 2000000 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 11:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.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 11:49:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:49:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:49:24: 3000000 INFO @ Tue, 02 Aug 2022 11:49:32: 1000000 INFO @ Tue, 02 Aug 2022 11:49:35: 4000000 INFO @ Tue, 02 Aug 2022 11:49:44: 2000000 INFO @ Tue, 02 Aug 2022 11:49:47: 5000000 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 11:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.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 11:49:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:49:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:49:56: 3000000 INFO @ Tue, 02 Aug 2022 11:49:58: 6000000 INFO @ Tue, 02 Aug 2022 11:50:01: 1000000 INFO @ Tue, 02 Aug 2022 11:50:09: 4000000 INFO @ Tue, 02 Aug 2022 11:50:11: 7000000 INFO @ Tue, 02 Aug 2022 11:50:13: 2000000 INFO @ Tue, 02 Aug 2022 11:50:21: 5000000 INFO @ Tue, 02 Aug 2022 11:50:23: 8000000 INFO @ Tue, 02 Aug 2022 11:50:24: 3000000 INFO @ Tue, 02 Aug 2022 11:50:33: 6000000 INFO @ Tue, 02 Aug 2022 11:50:35: 9000000 INFO @ Tue, 02 Aug 2022 11:50:36: 4000000 INFO @ Tue, 02 Aug 2022 11:50:45: 7000000 INFO @ Tue, 02 Aug 2022 11:50:47: 10000000 INFO @ Tue, 02 Aug 2022 11:50:48: 5000000 INFO @ Tue, 02 Aug 2022 11:50:57: 8000000 INFO @ Tue, 02 Aug 2022 11:50:59: 6000000 INFO @ Tue, 02 Aug 2022 11:50:59: 11000000 INFO @ Tue, 02 Aug 2022 11:51:08: 9000000 INFO @ Tue, 02 Aug 2022 11:51:11: 7000000 INFO @ Tue, 02 Aug 2022 11:51:12: 12000000 INFO @ Tue, 02 Aug 2022 11:51:21: 10000000 INFO @ Tue, 02 Aug 2022 11:51:21: 8000000 INFO @ Tue, 02 Aug 2022 11:51:24: 13000000 INFO @ Tue, 02 Aug 2022 11:51:33: 9000000 INFO @ Tue, 02 Aug 2022 11:51:33: 11000000 INFO @ Tue, 02 Aug 2022 11:51:36: 14000000 INFO @ Tue, 02 Aug 2022 11:51:44: 10000000 INFO @ Tue, 02 Aug 2022 11:51:47: 12000000 INFO @ Tue, 02 Aug 2022 11:51:48: 15000000 INFO @ Tue, 02 Aug 2022 11:51:56: 11000000 INFO @ Tue, 02 Aug 2022 11:52:00: 16000000 INFO @ Tue, 02 Aug 2022 11:52:01: 13000000 INFO @ Tue, 02 Aug 2022 11:52:08: 12000000 INFO @ Tue, 02 Aug 2022 11:52:12: 17000000 INFO @ Tue, 02 Aug 2022 11:52:14: 14000000 INFO @ Tue, 02 Aug 2022 11:52:20: 13000000 INFO @ Tue, 02 Aug 2022 11:52:23: 18000000 INFO @ Tue, 02 Aug 2022 11:52:26: 15000000 INFO @ Tue, 02 Aug 2022 11:52:31: 14000000 INFO @ Tue, 02 Aug 2022 11:52:35: 19000000 INFO @ Tue, 02 Aug 2022 11:52:39: 16000000 INFO @ Tue, 02 Aug 2022 11:52:43: 15000000 INFO @ Tue, 02 Aug 2022 11:52:46: 20000000 INFO @ Tue, 02 Aug 2022 11:52:52: 17000000 INFO @ Tue, 02 Aug 2022 11:52:54: 16000000 INFO @ Tue, 02 Aug 2022 11:52:58: 21000000 INFO @ Tue, 02 Aug 2022 11:53:04: 18000000 INFO @ Tue, 02 Aug 2022 11:53:06: 17000000 INFO @ Tue, 02 Aug 2022 11:53:09: 22000000 INFO @ Tue, 02 Aug 2022 11:53:17: 19000000 INFO @ Tue, 02 Aug 2022 11:53:17: 18000000 INFO @ Tue, 02 Aug 2022 11:53:22: 23000000 INFO @ Tue, 02 Aug 2022 11:53:30: 20000000 INFO @ Tue, 02 Aug 2022 11:53:30: 19000000 INFO @ Tue, 02 Aug 2022 11:53:34: 24000000 INFO @ Tue, 02 Aug 2022 11:53:41: 20000000 INFO @ Tue, 02 Aug 2022 11:53:42: 21000000 INFO @ Tue, 02 Aug 2022 11:53:46: 25000000 INFO @ Tue, 02 Aug 2022 11:53:52: 21000000 INFO @ Tue, 02 Aug 2022 11:53:54: 22000000 INFO @ Tue, 02 Aug 2022 11:53:59: 26000000 INFO @ Tue, 02 Aug 2022 11:54:04: 22000000 INFO @ Tue, 02 Aug 2022 11:54:08: 23000000 INFO @ Tue, 02 Aug 2022 11:54:11: 27000000 INFO @ Tue, 02 Aug 2022 11:54:16: 23000000 INFO @ Tue, 02 Aug 2022 11:54:20: 24000000 INFO @ Tue, 02 Aug 2022 11:54:23: 28000000 INFO @ Tue, 02 Aug 2022 11:54:28: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:54:31: 25000000 INFO @ Tue, 02 Aug 2022 11:54:35: 29000000 INFO @ Tue, 02 Aug 2022 11:54:40: 25000000 INFO @ Tue, 02 Aug 2022 11:54:43: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:54:43: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:54:43: #1 total tags in treatment: 8323360 INFO @ Tue, 02 Aug 2022 11:54:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:54:43: #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 11:54:43: #1 tags after filtering in treatment: 7601395 INFO @ Tue, 02 Aug 2022 11:54:43: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:54:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:54:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:54:44: #2 number of paired peaks: 575 WARNING @ Tue, 02 Aug 2022 11:54:44: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Tue, 02 Aug 2022 11:54:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:54:44: start X-correlation... INFO @ Tue, 02 Aug 2022 11:54:45: 26000000 INFO @ Tue, 02 Aug 2022 11:54:45: end of X-cor INFO @ Tue, 02 Aug 2022 11:54:45: #2 finished! INFO @ Tue, 02 Aug 2022 11:54:45: #2 predicted fragment length is 230 bps INFO @ Tue, 02 Aug 2022 11:54:45: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 02 Aug 2022 11:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.05_model.r WARNING @ Tue, 02 Aug 2022 11:54:45: #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 11:54:45: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Tue, 02 Aug 2022 11:54:45: #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 11:54:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:54:51: 26000000 INFO @ Tue, 02 Aug 2022 11:54:56: 27000000 INFO @ Tue, 02 Aug 2022 11:55:02: 27000000 INFO @ Tue, 02 Aug 2022 11:55:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:55:08: 28000000 INFO @ Tue, 02 Aug 2022 11:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.05_summits.bed INFO @ Tue, 02 Aug 2022 11:55:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:55:12: 28000000 INFO @ Tue, 02 Aug 2022 11:55:20: 29000000 INFO @ Tue, 02 Aug 2022 11:55:22: 29000000 INFO @ Tue, 02 Aug 2022 11:55:29: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:55:29: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:55:29: #1 total tags in treatment: 8323360 INFO @ Tue, 02 Aug 2022 11:55:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:55:29: #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 11:55:30: #1 tags after filtering in treatment: 7601395 INFO @ Tue, 02 Aug 2022 11:55:30: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:55:30: #1 finished! INFO @ Tue, 02 Aug 2022 11:55:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:55:30: #2 number of paired peaks: 575 WARNING @ Tue, 02 Aug 2022 11:55:30: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Tue, 02 Aug 2022 11:55:30: start model_add_line... INFO @ Tue, 02 Aug 2022 11:55:30: start X-correlation... INFO @ Tue, 02 Aug 2022 11:55:30: end of X-cor INFO @ Tue, 02 Aug 2022 11:55:30: #2 finished! INFO @ Tue, 02 Aug 2022 11:55:30: #2 predicted fragment length is 230 bps INFO @ Tue, 02 Aug 2022 11:55:30: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 02 Aug 2022 11:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.10_model.r WARNING @ Tue, 02 Aug 2022 11:55:30: #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 11:55:30: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Tue, 02 Aug 2022 11:55:30: #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 11:55:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:55:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:55:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:55:30: #1 total tags in treatment: 8323360 INFO @ Tue, 02 Aug 2022 11:55:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:55:30: #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 11:55:30: #1 tags after filtering in treatment: 7601395 INFO @ Tue, 02 Aug 2022 11:55:30: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:55:30: #1 finished! INFO @ Tue, 02 Aug 2022 11:55:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:55:31: #2 number of paired peaks: 575 WARNING @ Tue, 02 Aug 2022 11:55:31: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Tue, 02 Aug 2022 11:55:31: start model_add_line... INFO @ Tue, 02 Aug 2022 11:55:31: start X-correlation... INFO @ Tue, 02 Aug 2022 11:55:31: end of X-cor INFO @ Tue, 02 Aug 2022 11:55:31: #2 finished! INFO @ Tue, 02 Aug 2022 11:55:31: #2 predicted fragment length is 230 bps INFO @ Tue, 02 Aug 2022 11:55:31: #2 alternative fragment length(s) may be 230 bps INFO @ Tue, 02 Aug 2022 11:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.20_model.r WARNING @ Tue, 02 Aug 2022 11:55:31: #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 11:55:31: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Tue, 02 Aug 2022 11:55:31: #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 11:55:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:55:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:55:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.10_summits.bed INFO @ Tue, 02 Aug 2022 11:55:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336908/SRX13336908.20_summits.bed INFO @ Tue, 02 Aug 2022 11:55:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 50 millis CompletedMACS2peakCalling