Job ID = 14158382 SRX = SRX10641177 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18555619 spots for SRR14280101/SRR14280101.sra Written 18555619 spots for SRR14280101/SRR14280101.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158995 ("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: 00:28:27 18555619 reads; of these: 18555619 (100.00%) were paired; of these: 9124542 (49.17%) aligned concordantly 0 times 7981551 (43.01%) aligned concordantly exactly 1 time 1449526 (7.81%) aligned concordantly >1 times ---- 9124542 pairs aligned concordantly 0 times; of these: 2351061 (25.77%) aligned discordantly 1 time ---- 6773481 pairs aligned 0 times concordantly or discordantly; of these: 13546962 mates make up the pairs; of these: 12412215 (91.62%) aligned 0 times 597689 (4.41%) aligned exactly 1 time 537058 (3.96%) aligned >1 times 66.55% overall alignment rate Time searching: 00:28:27 Overall time: 00:28:27 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 20 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] 1501091 / 11739151 = 0.1279 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 17:15:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.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 17:15:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:15:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:15:36: 1000000 INFO @ Wed, 08 Dec 2021 17:15:44: 2000000 INFO @ Wed, 08 Dec 2021 17:15:52: 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 17:15:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.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 17:15:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:15:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:16:00: 4000000 INFO @ Wed, 08 Dec 2021 17:16:07: 1000000 INFO @ Wed, 08 Dec 2021 17:16:09: 5000000 INFO @ Wed, 08 Dec 2021 17:16:16: 2000000 INFO @ Wed, 08 Dec 2021 17:16:18: 6000000 INFO @ Wed, 08 Dec 2021 17:16:25: 3000000 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 17:16:27: 7000000 INFO @ Wed, 08 Dec 2021 17:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.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 17:16:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:16:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:16:34: 4000000 INFO @ Wed, 08 Dec 2021 17:16:36: 8000000 INFO @ Wed, 08 Dec 2021 17:16:37: 1000000 INFO @ Wed, 08 Dec 2021 17:16:43: 5000000 INFO @ Wed, 08 Dec 2021 17:16:45: 9000000 INFO @ Wed, 08 Dec 2021 17:16:46: 2000000 INFO @ Wed, 08 Dec 2021 17:16:52: 6000000 INFO @ Wed, 08 Dec 2021 17:16:54: 10000000 INFO @ Wed, 08 Dec 2021 17:16:56: 3000000 INFO @ Wed, 08 Dec 2021 17:17:02: 7000000 INFO @ Wed, 08 Dec 2021 17:17:03: 11000000 INFO @ Wed, 08 Dec 2021 17:17:05: 4000000 INFO @ Wed, 08 Dec 2021 17:17:11: 8000000 INFO @ Wed, 08 Dec 2021 17:17:12: 12000000 INFO @ Wed, 08 Dec 2021 17:17:14: 5000000 INFO @ Wed, 08 Dec 2021 17:17:20: 9000000 INFO @ Wed, 08 Dec 2021 17:17:22: 13000000 INFO @ Wed, 08 Dec 2021 17:17:23: 6000000 INFO @ Wed, 08 Dec 2021 17:17:29: 10000000 INFO @ Wed, 08 Dec 2021 17:17:31: 14000000 INFO @ Wed, 08 Dec 2021 17:17:33: 7000000 INFO @ Wed, 08 Dec 2021 17:17:38: 11000000 INFO @ Wed, 08 Dec 2021 17:17:40: 15000000 INFO @ Wed, 08 Dec 2021 17:17:42: 8000000 INFO @ Wed, 08 Dec 2021 17:17:47: 12000000 INFO @ Wed, 08 Dec 2021 17:17:49: 16000000 INFO @ Wed, 08 Dec 2021 17:17:51: 9000000 INFO @ Wed, 08 Dec 2021 17:17:56: 13000000 INFO @ Wed, 08 Dec 2021 17:17:58: 17000000 INFO @ Wed, 08 Dec 2021 17:18:00: 10000000 INFO @ Wed, 08 Dec 2021 17:18:05: 14000000 INFO @ Wed, 08 Dec 2021 17:18:07: 18000000 INFO @ Wed, 08 Dec 2021 17:18:09: 11000000 INFO @ Wed, 08 Dec 2021 17:18:14: 15000000 INFO @ Wed, 08 Dec 2021 17:18:16: 19000000 INFO @ Wed, 08 Dec 2021 17:18:18: 12000000 INFO @ Wed, 08 Dec 2021 17:18:23: 16000000 INFO @ Wed, 08 Dec 2021 17:18:25: 20000000 INFO @ Wed, 08 Dec 2021 17:18:27: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:18:32: 17000000 INFO @ Wed, 08 Dec 2021 17:18:34: 21000000 INFO @ Wed, 08 Dec 2021 17:18:36: 14000000 INFO @ Wed, 08 Dec 2021 17:18:41: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:18:41: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:18:41: #1 total tags in treatment: 8163718 INFO @ Wed, 08 Dec 2021 17:18:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:18:41: #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 17:18:41: #1 tags after filtering in treatment: 7441677 INFO @ Wed, 08 Dec 2021 17:18:41: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 17:18:41: #1 finished! INFO @ Wed, 08 Dec 2021 17:18:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:18:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:18:41: 18000000 INFO @ Wed, 08 Dec 2021 17:18:41: #2 number of paired peaks: 534 WARNING @ Wed, 08 Dec 2021 17:18:41: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Wed, 08 Dec 2021 17:18:41: start model_add_line... INFO @ Wed, 08 Dec 2021 17:18:41: start X-correlation... INFO @ Wed, 08 Dec 2021 17:18:41: end of X-cor INFO @ Wed, 08 Dec 2021 17:18:41: #2 finished! INFO @ Wed, 08 Dec 2021 17:18:41: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:18:41: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:18:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.05_model.r WARNING @ Wed, 08 Dec 2021 17:18:41: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:18:41: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:18:41: #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 17:18:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:18:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:18:45: 15000000 INFO @ Wed, 08 Dec 2021 17:18:50: 19000000 INFO @ Wed, 08 Dec 2021 17:18:54: 16000000 INFO @ Wed, 08 Dec 2021 17:18:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:18:59: 20000000 INFO @ Wed, 08 Dec 2021 17:19:03: 17000000 INFO @ Wed, 08 Dec 2021 17:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.05_summits.bed INFO @ Wed, 08 Dec 2021 17:19:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:19:08: 21000000 INFO @ Wed, 08 Dec 2021 17:19:12: 18000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:19:14: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:19:14: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:19:14: #1 total tags in treatment: 8163718 INFO @ Wed, 08 Dec 2021 17:19:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:19:14: #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 17:19:14: #1 tags after filtering in treatment: 7441677 INFO @ Wed, 08 Dec 2021 17:19:14: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 17:19:14: #1 finished! INFO @ Wed, 08 Dec 2021 17:19:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:19:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:19:14: #2 number of paired peaks: 534 WARNING @ Wed, 08 Dec 2021 17:19:14: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Wed, 08 Dec 2021 17:19:14: start model_add_line... INFO @ Wed, 08 Dec 2021 17:19:14: start X-correlation... INFO @ Wed, 08 Dec 2021 17:19:14: end of X-cor INFO @ Wed, 08 Dec 2021 17:19:14: #2 finished! INFO @ Wed, 08 Dec 2021 17:19:14: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:19:14: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:19:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.10_model.r WARNING @ Wed, 08 Dec 2021 17:19:14: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:19:14: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:19:14: #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 17:19:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:19:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:19:20: 19000000 INFO @ Wed, 08 Dec 2021 17:19:28: 20000000 INFO @ Wed, 08 Dec 2021 17:19:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:19:35: 21000000 INFO @ Wed, 08 Dec 2021 17:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.10_summits.bed INFO @ Wed, 08 Dec 2021 17:19:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:19:41: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:19:41: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:19:41: #1 total tags in treatment: 8163718 INFO @ Wed, 08 Dec 2021 17:19:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:19:41: #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 17:19:41: #1 tags after filtering in treatment: 7441677 INFO @ Wed, 08 Dec 2021 17:19:41: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 17:19:41: #1 finished! INFO @ Wed, 08 Dec 2021 17:19:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:19:41: #2 number of paired peaks: 534 WARNING @ Wed, 08 Dec 2021 17:19:41: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Wed, 08 Dec 2021 17:19:41: start model_add_line... INFO @ Wed, 08 Dec 2021 17:19:41: start X-correlation... INFO @ Wed, 08 Dec 2021 17:19:41: end of X-cor INFO @ Wed, 08 Dec 2021 17:19:41: #2 finished! INFO @ Wed, 08 Dec 2021 17:19:41: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 17:19:41: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 17:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.20_model.r WARNING @ Wed, 08 Dec 2021 17:19:41: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:19:41: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 17:19:41: #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 17:19:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:19:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641177/SRX10641177.20_summits.bed INFO @ Wed, 08 Dec 2021 17:20:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling