Job ID = 16432892 SRX = SRX13336902 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24632080 spots for SRR17152886/SRR17152886.sra Written 24632080 spots for SRR17152886/SRR17152886.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435252 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:00:26 24632080 reads; of these: 24632080 (100.00%) were paired; of these: 11732644 (47.63%) aligned concordantly 0 times 10960241 (44.50%) aligned concordantly exactly 1 time 1939195 (7.87%) aligned concordantly >1 times ---- 11732644 pairs aligned concordantly 0 times; of these: 5263888 (44.87%) aligned discordantly 1 time ---- 6468756 pairs aligned 0 times concordantly or discordantly; of these: 12937512 mates make up the pairs; of these: 10962962 (84.74%) aligned 0 times 923660 (7.14%) aligned exactly 1 time 1050890 (8.12%) aligned >1 times 77.75% overall alignment rate Time searching: 01:00:26 Overall time: 01:00:26 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] 1712257 / 18106347 = 0.0946 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 11:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.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 11:01:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:35: 1000000 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 11:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.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 11:01:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:51: 2000000 INFO @ Tue, 02 Aug 2022 11:02:04: 1000000 INFO @ Tue, 02 Aug 2022 11:02:06: 3000000 INFO @ Tue, 02 Aug 2022 11:02:17: 2000000 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 11:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.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 11:02:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:02:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:02:23: 4000000 INFO @ Tue, 02 Aug 2022 11:02:27: 3000000 INFO @ Tue, 02 Aug 2022 11:02:37: 1000000 INFO @ Tue, 02 Aug 2022 11:02:38: 4000000 INFO @ Tue, 02 Aug 2022 11:02:39: 5000000 INFO @ Tue, 02 Aug 2022 11:02:49: 5000000 INFO @ Tue, 02 Aug 2022 11:02:55: 6000000 INFO @ Tue, 02 Aug 2022 11:02:55: 2000000 INFO @ Tue, 02 Aug 2022 11:03:01: 6000000 INFO @ Tue, 02 Aug 2022 11:03:11: 7000000 INFO @ Tue, 02 Aug 2022 11:03:12: 7000000 INFO @ Tue, 02 Aug 2022 11:03:12: 3000000 INFO @ Tue, 02 Aug 2022 11:03:25: 8000000 INFO @ Tue, 02 Aug 2022 11:03:29: 8000000 INFO @ Tue, 02 Aug 2022 11:03:30: 4000000 INFO @ Tue, 02 Aug 2022 11:03:38: 9000000 INFO @ Tue, 02 Aug 2022 11:03:46: 9000000 INFO @ Tue, 02 Aug 2022 11:03:48: 5000000 INFO @ Tue, 02 Aug 2022 11:03:50: 10000000 INFO @ Tue, 02 Aug 2022 11:04:03: 10000000 INFO @ Tue, 02 Aug 2022 11:04:03: 11000000 INFO @ Tue, 02 Aug 2022 11:04:05: 6000000 INFO @ Tue, 02 Aug 2022 11:04:15: 12000000 INFO @ Tue, 02 Aug 2022 11:04:21: 11000000 INFO @ Tue, 02 Aug 2022 11:04:23: 7000000 INFO @ Tue, 02 Aug 2022 11:04:26: 13000000 INFO @ Tue, 02 Aug 2022 11:04:37: 14000000 INFO @ Tue, 02 Aug 2022 11:04:38: 12000000 INFO @ Tue, 02 Aug 2022 11:04:40: 8000000 INFO @ Tue, 02 Aug 2022 11:04:49: 15000000 INFO @ Tue, 02 Aug 2022 11:04:55: 13000000 INFO @ Tue, 02 Aug 2022 11:04:57: 9000000 INFO @ Tue, 02 Aug 2022 11:05:00: 16000000 INFO @ Tue, 02 Aug 2022 11:05:11: 14000000 INFO @ Tue, 02 Aug 2022 11:05:13: 17000000 INFO @ Tue, 02 Aug 2022 11:05:14: 10000000 INFO @ Tue, 02 Aug 2022 11:05:25: 18000000 INFO @ Tue, 02 Aug 2022 11:05:28: 15000000 INFO @ Tue, 02 Aug 2022 11:05:31: 11000000 INFO @ Tue, 02 Aug 2022 11:05:37: 19000000 INFO @ Tue, 02 Aug 2022 11:05:45: 16000000 INFO @ Tue, 02 Aug 2022 11:05:48: 12000000 INFO @ Tue, 02 Aug 2022 11:05:49: 20000000 INFO @ Tue, 02 Aug 2022 11:06:00: 21000000 INFO @ Tue, 02 Aug 2022 11:06:02: 17000000 INFO @ Tue, 02 Aug 2022 11:06:06: 13000000 INFO @ Tue, 02 Aug 2022 11:06:11: 22000000 INFO @ Tue, 02 Aug 2022 11:06:19: 18000000 INFO @ Tue, 02 Aug 2022 11:06:23: 23000000 INFO @ Tue, 02 Aug 2022 11:06:23: 14000000 INFO @ Tue, 02 Aug 2022 11:06:34: 24000000 INFO @ Tue, 02 Aug 2022 11:06:36: 19000000 INFO @ Tue, 02 Aug 2022 11:06:40: 15000000 INFO @ Tue, 02 Aug 2022 11:06:46: 25000000 INFO @ Tue, 02 Aug 2022 11:06:53: 20000000 INFO @ Tue, 02 Aug 2022 11:06:57: 16000000 INFO @ Tue, 02 Aug 2022 11:06:58: 26000000 INFO @ Tue, 02 Aug 2022 11:07:09: 21000000 INFO @ Tue, 02 Aug 2022 11:07:10: 27000000 INFO @ Tue, 02 Aug 2022 11:07:13: 17000000 INFO @ Tue, 02 Aug 2022 11:07:21: 28000000 INFO @ Tue, 02 Aug 2022 11:07:26: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:07:30: 18000000 INFO @ Tue, 02 Aug 2022 11:07:32: 29000000 INFO @ Tue, 02 Aug 2022 11:07:42: 23000000 INFO @ Tue, 02 Aug 2022 11:07:42: 30000000 INFO @ Tue, 02 Aug 2022 11:07:46: 19000000 INFO @ Tue, 02 Aug 2022 11:07:53: 31000000 INFO @ Tue, 02 Aug 2022 11:07:57: 24000000 INFO @ Tue, 02 Aug 2022 11:08:02: 20000000 INFO @ Tue, 02 Aug 2022 11:08:02: 32000000 INFO @ Tue, 02 Aug 2022 11:08:11: 33000000 INFO @ Tue, 02 Aug 2022 11:08:13: 25000000 INFO @ Tue, 02 Aug 2022 11:08:18: 21000000 INFO @ Tue, 02 Aug 2022 11:08:21: 34000000 INFO @ Tue, 02 Aug 2022 11:08:29: 26000000 INFO @ Tue, 02 Aug 2022 11:08:29: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:08:29: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:08:29: #1 total tags in treatment: 11570259 INFO @ Tue, 02 Aug 2022 11:08:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:08:29: #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 11:08:29: #1 tags after filtering in treatment: 10509213 INFO @ Tue, 02 Aug 2022 11:08:29: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:08:29: #1 finished! INFO @ Tue, 02 Aug 2022 11:08:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:08:30: #2 number of paired peaks: 480 WARNING @ Tue, 02 Aug 2022 11:08:30: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Tue, 02 Aug 2022 11:08:30: start model_add_line... INFO @ Tue, 02 Aug 2022 11:08:30: start X-correlation... INFO @ Tue, 02 Aug 2022 11:08:30: end of X-cor INFO @ Tue, 02 Aug 2022 11:08:30: #2 finished! INFO @ Tue, 02 Aug 2022 11:08:30: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 11:08:30: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 11:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.10_model.r WARNING @ Tue, 02 Aug 2022 11:08:30: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:08:30: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 11:08:30: #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 11:08:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:08:34: 22000000 INFO @ Tue, 02 Aug 2022 11:08:44: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:08:49: 23000000 INFO @ Tue, 02 Aug 2022 11:08:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:08:59: 28000000 INFO @ Tue, 02 Aug 2022 11:09:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.10_summits.bed INFO @ Tue, 02 Aug 2022 11:09:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:09:04: 24000000 INFO @ Tue, 02 Aug 2022 11:09:15: 29000000 INFO @ Tue, 02 Aug 2022 11:09:20: 25000000 INFO @ Tue, 02 Aug 2022 11:09:31: 30000000 INFO @ Tue, 02 Aug 2022 11:09:35: 26000000 INFO @ Tue, 02 Aug 2022 11:09:46: 31000000 INFO @ Tue, 02 Aug 2022 11:09:51: 27000000 INFO @ Tue, 02 Aug 2022 11:10:02: 32000000 INFO @ Tue, 02 Aug 2022 11:10:06: 28000000 INFO @ Tue, 02 Aug 2022 11:10:17: 33000000 INFO @ Tue, 02 Aug 2022 11:10:22: 29000000 INFO @ Tue, 02 Aug 2022 11:10:32: 34000000 INFO @ Tue, 02 Aug 2022 11:10:36: 30000000 INFO @ Tue, 02 Aug 2022 11:10:44: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:10:44: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:10:44: #1 total tags in treatment: 11570259 INFO @ Tue, 02 Aug 2022 11:10:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:10:44: #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 11:10:44: #1 tags after filtering in treatment: 10509213 INFO @ Tue, 02 Aug 2022 11:10:44: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:10:44: #1 finished! INFO @ Tue, 02 Aug 2022 11:10:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:10:45: #2 number of paired peaks: 480 WARNING @ Tue, 02 Aug 2022 11:10:45: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Tue, 02 Aug 2022 11:10:45: start model_add_line... INFO @ Tue, 02 Aug 2022 11:10:45: start X-correlation... INFO @ Tue, 02 Aug 2022 11:10:45: end of X-cor INFO @ Tue, 02 Aug 2022 11:10:45: #2 finished! INFO @ Tue, 02 Aug 2022 11:10:45: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 11:10:45: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 11:10:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.05_model.r WARNING @ Tue, 02 Aug 2022 11:10:45: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:10:45: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 11:10:45: #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 11:10:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:10:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:10:50: 31000000 INFO @ Tue, 02 Aug 2022 11:11:04: 32000000 INFO @ Tue, 02 Aug 2022 11:11:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:11:17: 33000000 INFO @ Tue, 02 Aug 2022 11:11:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:11:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:11:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.05_summits.bed INFO @ Tue, 02 Aug 2022 11:11:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (490 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:11:29: 34000000 INFO @ Tue, 02 Aug 2022 11:11:40: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:11:40: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:11:40: #1 total tags in treatment: 11570259 INFO @ Tue, 02 Aug 2022 11:11:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:11:40: #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 11:11:40: #1 tags after filtering in treatment: 10509213 INFO @ Tue, 02 Aug 2022 11:11:40: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:11:40: #1 finished! INFO @ Tue, 02 Aug 2022 11:11:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:11:41: #2 number of paired peaks: 480 WARNING @ Tue, 02 Aug 2022 11:11:41: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Tue, 02 Aug 2022 11:11:41: start model_add_line... INFO @ Tue, 02 Aug 2022 11:11:41: start X-correlation... INFO @ Tue, 02 Aug 2022 11:11:41: end of X-cor INFO @ Tue, 02 Aug 2022 11:11:41: #2 finished! INFO @ Tue, 02 Aug 2022 11:11:41: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 11:11:41: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 11:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.20_model.r WARNING @ Tue, 02 Aug 2022 11:11:41: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:11:41: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 11:11:41: #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 11:11:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:12:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336902/SRX13336902.20_summits.bed INFO @ Tue, 02 Aug 2022 11:12:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 114 millis CompletedMACS2peakCalling