Job ID = 14158028 SRX = SRX10641219 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16788522 spots for SRR14280059/SRR14280059.sra Written 16788522 spots for SRR14280059/SRR14280059.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158386 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:32:57 16788522 reads; of these: 16788522 (100.00%) were paired; of these: 8137972 (48.47%) aligned concordantly 0 times 7331859 (43.67%) aligned concordantly exactly 1 time 1318691 (7.85%) aligned concordantly >1 times ---- 8137972 pairs aligned concordantly 0 times; of these: 1914994 (23.53%) aligned discordantly 1 time ---- 6222978 pairs aligned 0 times concordantly or discordantly; of these: 12445956 mates make up the pairs; of these: 11593561 (93.15%) aligned 0 times 432714 (3.48%) aligned exactly 1 time 419681 (3.37%) aligned >1 times 65.47% overall alignment rate Time searching: 00:32:58 Overall time: 00:32:58 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] 1278921 / 10521958 = 0.1215 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 14:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.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 14:47:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:47:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:48:13: 1000000 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 14:48:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.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 14:48:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:48:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:48:29: 2000000 INFO @ Wed, 08 Dec 2021 14:48:39: 1000000 INFO @ Wed, 08 Dec 2021 14:48:45: 3000000 INFO @ Wed, 08 Dec 2021 14:48:51: 2000000 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 14:48:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.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 14:48:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:48:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:49:01: 4000000 INFO @ Wed, 08 Dec 2021 14:49:03: 3000000 INFO @ Wed, 08 Dec 2021 14:49:15: 1000000 INFO @ Wed, 08 Dec 2021 14:49:15: 4000000 INFO @ Wed, 08 Dec 2021 14:49:16: 5000000 INFO @ Wed, 08 Dec 2021 14:49:27: 5000000 INFO @ Wed, 08 Dec 2021 14:49:32: 6000000 INFO @ Wed, 08 Dec 2021 14:49:32: 2000000 INFO @ Wed, 08 Dec 2021 14:49:40: 6000000 INFO @ Wed, 08 Dec 2021 14:49:48: 7000000 INFO @ Wed, 08 Dec 2021 14:49:49: 3000000 INFO @ Wed, 08 Dec 2021 14:49:53: 7000000 INFO @ Wed, 08 Dec 2021 14:50:04: 8000000 INFO @ Wed, 08 Dec 2021 14:50:06: 4000000 INFO @ Wed, 08 Dec 2021 14:50:07: 8000000 INFO @ Wed, 08 Dec 2021 14:50:19: 9000000 INFO @ Wed, 08 Dec 2021 14:50:20: 9000000 INFO @ Wed, 08 Dec 2021 14:50:23: 5000000 INFO @ Wed, 08 Dec 2021 14:50:33: 10000000 INFO @ Wed, 08 Dec 2021 14:50:35: 10000000 INFO @ Wed, 08 Dec 2021 14:50:39: 6000000 INFO @ Wed, 08 Dec 2021 14:50:46: 11000000 INFO @ Wed, 08 Dec 2021 14:50:50: 11000000 INFO @ Wed, 08 Dec 2021 14:50:56: 7000000 INFO @ Wed, 08 Dec 2021 14:50:58: 12000000 INFO @ Wed, 08 Dec 2021 14:51:06: 12000000 INFO @ Wed, 08 Dec 2021 14:51:11: 13000000 INFO @ Wed, 08 Dec 2021 14:51:12: 8000000 INFO @ Wed, 08 Dec 2021 14:51:22: 13000000 INFO @ Wed, 08 Dec 2021 14:51:24: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:51:29: 9000000 INFO @ Wed, 08 Dec 2021 14:51:36: 15000000 INFO @ Wed, 08 Dec 2021 14:51:37: 14000000 INFO @ Wed, 08 Dec 2021 14:51:45: 10000000 INFO @ Wed, 08 Dec 2021 14:51:49: 16000000 INFO @ Wed, 08 Dec 2021 14:51:53: 15000000 INFO @ Wed, 08 Dec 2021 14:52:01: 11000000 INFO @ Wed, 08 Dec 2021 14:52:02: 17000000 INFO @ Wed, 08 Dec 2021 14:52:09: 16000000 INFO @ Wed, 08 Dec 2021 14:52:16: 18000000 INFO @ Wed, 08 Dec 2021 14:52:18: 12000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:52:25: 17000000 INFO @ Wed, 08 Dec 2021 14:52:30: 19000000 INFO @ Wed, 08 Dec 2021 14:52:34: 13000000 INFO @ Wed, 08 Dec 2021 14:52:36: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:52:36: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:52:36: #1 total tags in treatment: 7554089 INFO @ Wed, 08 Dec 2021 14:52:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:52:36: #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 14:52:36: #1 tags after filtering in treatment: 6932926 INFO @ Wed, 08 Dec 2021 14:52:36: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:52:36: #1 finished! INFO @ Wed, 08 Dec 2021 14:52:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:52:36: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 14:52:36: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 14:52:36: start model_add_line... INFO @ Wed, 08 Dec 2021 14:52:36: start X-correlation... INFO @ Wed, 08 Dec 2021 14:52:36: end of X-cor INFO @ Wed, 08 Dec 2021 14:52:36: #2 finished! INFO @ Wed, 08 Dec 2021 14:52:36: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 14:52:36: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 14:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.10_model.r WARNING @ Wed, 08 Dec 2021 14:52:37: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:52:37: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 14:52:37: #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 14:52:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:52:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:52:41: 18000000 INFO @ Wed, 08 Dec 2021 14:52:50: 14000000 INFO @ Wed, 08 Dec 2021 14:52:56: 19000000 INFO @ Wed, 08 Dec 2021 14:52:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:53:02: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:53:02: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:53:02: #1 total tags in treatment: 7554089 INFO @ Wed, 08 Dec 2021 14:53:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:53:02: #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 14:53:02: #1 tags after filtering in treatment: 6932926 INFO @ Wed, 08 Dec 2021 14:53:02: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:53:02: #1 finished! INFO @ Wed, 08 Dec 2021 14:53:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:53:03: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 14:53:03: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 14:53:03: start model_add_line... INFO @ Wed, 08 Dec 2021 14:53:03: start X-correlation... INFO @ Wed, 08 Dec 2021 14:53:03: end of X-cor INFO @ Wed, 08 Dec 2021 14:53:03: #2 finished! INFO @ Wed, 08 Dec 2021 14:53:03: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 14:53:03: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 14:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.05_model.r WARNING @ Wed, 08 Dec 2021 14:53:03: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:53:03: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 14:53:03: #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 14:53:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:53:05: 15000000 INFO @ Wed, 08 Dec 2021 14:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.10_summits.bed INFO @ Wed, 08 Dec 2021 14:53:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:53:21: 16000000 INFO @ Wed, 08 Dec 2021 14:53:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:53:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.05_summits.bed INFO @ Wed, 08 Dec 2021 14:53:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:53:36: 17000000 INFO @ Wed, 08 Dec 2021 14:53:51: 18000000 INFO @ Wed, 08 Dec 2021 14:54:06: 19000000 INFO @ Wed, 08 Dec 2021 14:54:12: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:54:12: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:54:12: #1 total tags in treatment: 7554089 INFO @ Wed, 08 Dec 2021 14:54:12: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:54:12: #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 14:54:12: #1 tags after filtering in treatment: 6932926 INFO @ Wed, 08 Dec 2021 14:54:12: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:54:12: #1 finished! INFO @ Wed, 08 Dec 2021 14:54:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:54:13: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 14:54:13: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 14:54:13: start model_add_line... INFO @ Wed, 08 Dec 2021 14:54:13: start X-correlation... INFO @ Wed, 08 Dec 2021 14:54:13: end of X-cor INFO @ Wed, 08 Dec 2021 14:54:13: #2 finished! INFO @ Wed, 08 Dec 2021 14:54:13: #2 predicted fragment length is 217 bps INFO @ Wed, 08 Dec 2021 14:54:13: #2 alternative fragment length(s) may be 217 bps INFO @ Wed, 08 Dec 2021 14:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.20_model.r WARNING @ Wed, 08 Dec 2021 14:54:13: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:54:13: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Wed, 08 Dec 2021 14:54:13: #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 14:54:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:54:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641219/SRX10641219.20_summits.bed INFO @ Wed, 08 Dec 2021 14:54:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 2 millis CompletedMACS2peakCalling