Job ID = 14158377 SRX = SRX10641174 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T07:31:01 prefetch.2.10.7: 1) Downloading 'SRR14280104'... 2021-12-08T07:31:01 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T08:02:19 prefetch.2.10.7: HTTPS download succeed 2021-12-08T08:02:19 prefetch.2.10.7: 1) 'SRR14280104' was downloaded successfully 2021-12-08T08:02:19 prefetch.2.10.7: 'SRR14280104' has 0 unresolved dependencies Read 15700166 spots for SRR14280104/SRR14280104.sra Written 15700166 spots for SRR14280104/SRR14280104.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159056 ("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: 00:23:41 15700166 reads; of these: 15700166 (100.00%) were paired; of these: 7728399 (49.22%) aligned concordantly 0 times 6728202 (42.85%) aligned concordantly exactly 1 time 1243565 (7.92%) aligned concordantly >1 times ---- 7728399 pairs aligned concordantly 0 times; of these: 2105185 (27.24%) aligned discordantly 1 time ---- 5623214 pairs aligned 0 times concordantly or discordantly; of these: 11246428 mates make up the pairs; of these: 10337480 (91.92%) aligned 0 times 435402 (3.87%) aligned exactly 1 time 473546 (4.21%) aligned >1 times 67.08% overall alignment rate Time searching: 00:23:41 Overall time: 00:23:41 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] 1110418 / 10044250 = 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 17:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.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 17:37:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:37:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:38:08: 1000000 INFO @ Wed, 08 Dec 2021 17:38:16: 2000000 INFO @ Wed, 08 Dec 2021 17:38:24: 3000000 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 17:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.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 17:38:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:38:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:38:33: 4000000 INFO @ Wed, 08 Dec 2021 17:38:39: 1000000 INFO @ Wed, 08 Dec 2021 17:38:43: 5000000 INFO @ Wed, 08 Dec 2021 17:38:49: 2000000 INFO @ Wed, 08 Dec 2021 17:38:53: 6000000 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 17:38:59: 3000000 INFO @ Wed, 08 Dec 2021 17:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.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 17:38:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:38:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:39:03: 7000000 INFO @ Wed, 08 Dec 2021 17:39:09: 4000000 INFO @ Wed, 08 Dec 2021 17:39:09: 1000000 INFO @ Wed, 08 Dec 2021 17:39:13: 8000000 INFO @ Wed, 08 Dec 2021 17:39:19: 5000000 INFO @ Wed, 08 Dec 2021 17:39:19: 2000000 INFO @ Wed, 08 Dec 2021 17:39:23: 9000000 INFO @ Wed, 08 Dec 2021 17:39:29: 6000000 INFO @ Wed, 08 Dec 2021 17:39:30: 3000000 INFO @ Wed, 08 Dec 2021 17:39:33: 10000000 INFO @ Wed, 08 Dec 2021 17:39:40: 4000000 INFO @ Wed, 08 Dec 2021 17:39:40: 7000000 INFO @ Wed, 08 Dec 2021 17:39:43: 11000000 INFO @ Wed, 08 Dec 2021 17:39:50: 5000000 INFO @ Wed, 08 Dec 2021 17:39:50: 8000000 INFO @ Wed, 08 Dec 2021 17:39:53: 12000000 INFO @ Wed, 08 Dec 2021 17:40:00: 6000000 INFO @ Wed, 08 Dec 2021 17:40:00: 9000000 INFO @ Wed, 08 Dec 2021 17:40:03: 13000000 INFO @ Wed, 08 Dec 2021 17:40:11: 10000000 INFO @ Wed, 08 Dec 2021 17:40:11: 7000000 INFO @ Wed, 08 Dec 2021 17:40:13: 14000000 INFO @ Wed, 08 Dec 2021 17:40:21: 11000000 INFO @ Wed, 08 Dec 2021 17:40:21: 8000000 INFO @ Wed, 08 Dec 2021 17:40:23: 15000000 INFO @ Wed, 08 Dec 2021 17:40:31: 12000000 INFO @ Wed, 08 Dec 2021 17:40:31: 9000000 INFO @ Wed, 08 Dec 2021 17:40:33: 16000000 INFO @ Wed, 08 Dec 2021 17:40:41: 13000000 INFO @ Wed, 08 Dec 2021 17:40:41: 10000000 INFO @ Wed, 08 Dec 2021 17:40:43: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:40:52: 14000000 INFO @ Wed, 08 Dec 2021 17:40:52: 11000000 INFO @ Wed, 08 Dec 2021 17:40:53: 18000000 INFO @ Wed, 08 Dec 2021 17:41:02: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:41:02: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:41:02: #1 total tags in treatment: 7040350 INFO @ Wed, 08 Dec 2021 17:41:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:41:02: #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 17:41:02: #1 tags after filtering in treatment: 6544860 INFO @ Wed, 08 Dec 2021 17:41:02: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:41:02: #1 finished! INFO @ Wed, 08 Dec 2021 17:41:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:41:03: #2 number of paired peaks: 504 WARNING @ Wed, 08 Dec 2021 17:41:03: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Wed, 08 Dec 2021 17:41:03: start model_add_line... INFO @ Wed, 08 Dec 2021 17:41:03: start X-correlation... INFO @ Wed, 08 Dec 2021 17:41:03: end of X-cor INFO @ Wed, 08 Dec 2021 17:41:03: #2 finished! INFO @ Wed, 08 Dec 2021 17:41:03: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 17:41:03: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 17:41:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.05_model.r WARNING @ Wed, 08 Dec 2021 17:41:03: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:41:03: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 17:41:03: #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 17:41:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:41:03: 15000000 INFO @ Wed, 08 Dec 2021 17:41:03: 12000000 INFO @ Wed, 08 Dec 2021 17:41:13: 16000000 INFO @ Wed, 08 Dec 2021 17:41:13: 13000000 INFO @ Wed, 08 Dec 2021 17:41:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.05_summits.bed INFO @ Wed, 08 Dec 2021 17:41:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:41:24: 14000000 INFO @ Wed, 08 Dec 2021 17:41:24: 17000000 INFO @ Wed, 08 Dec 2021 17:41:34: 18000000 INFO @ Wed, 08 Dec 2021 17:41:34: 15000000 INFO @ Wed, 08 Dec 2021 17:41:42: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:41:42: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:41:42: #1 total tags in treatment: 7040350 INFO @ Wed, 08 Dec 2021 17:41:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:41:42: #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 17:41:42: #1 tags after filtering in treatment: 6544860 INFO @ Wed, 08 Dec 2021 17:41:42: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:41:42: #1 finished! INFO @ Wed, 08 Dec 2021 17:41:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:41:43: #2 number of paired peaks: 504 WARNING @ Wed, 08 Dec 2021 17:41:43: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Wed, 08 Dec 2021 17:41:43: start model_add_line... INFO @ Wed, 08 Dec 2021 17:41:43: start X-correlation... INFO @ Wed, 08 Dec 2021 17:41:43: end of X-cor INFO @ Wed, 08 Dec 2021 17:41:43: #2 finished! INFO @ Wed, 08 Dec 2021 17:41:43: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 17:41:43: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 17:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.10_model.r WARNING @ Wed, 08 Dec 2021 17:41:43: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:41:43: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 17:41:43: #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 17:41:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:41:44: 16000000 INFO @ Wed, 08 Dec 2021 17:41:53: 17000000 INFO @ Wed, 08 Dec 2021 17:41:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:42:03: 18000000 INFO @ Wed, 08 Dec 2021 17:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.10_summits.bed INFO @ Wed, 08 Dec 2021 17:42:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:42:10: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:42:10: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:42:10: #1 total tags in treatment: 7040350 INFO @ Wed, 08 Dec 2021 17:42:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:42:10: #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 17:42:10: #1 tags after filtering in treatment: 6544860 INFO @ Wed, 08 Dec 2021 17:42:10: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 17:42:10: #1 finished! INFO @ Wed, 08 Dec 2021 17:42:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:42:11: #2 number of paired peaks: 504 WARNING @ Wed, 08 Dec 2021 17:42:11: Fewer paired peaks (504) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 504 pairs to build model! INFO @ Wed, 08 Dec 2021 17:42:11: start model_add_line... INFO @ Wed, 08 Dec 2021 17:42:11: start X-correlation... INFO @ Wed, 08 Dec 2021 17:42:11: end of X-cor INFO @ Wed, 08 Dec 2021 17:42:11: #2 finished! INFO @ Wed, 08 Dec 2021 17:42:11: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 17:42:11: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 17:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.20_model.r WARNING @ Wed, 08 Dec 2021 17:42:11: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:42:11: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 17:42:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 17:42:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:42:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641174/SRX10641174.20_summits.bed INFO @ Wed, 08 Dec 2021 17:42:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 2 millis CompletedMACS2peakCalling