Job ID = 14158380 SRX = SRX10641176 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14155663 spots for SRR14280102/SRR14280102.sra Written 14155663 spots for SRR14280102/SRR14280102.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158994 ("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: 00:28:44 14155663 reads; of these: 14155663 (100.00%) were paired; of these: 7539230 (53.26%) aligned concordantly 0 times 5570790 (39.35%) aligned concordantly exactly 1 time 1045643 (7.39%) aligned concordantly >1 times ---- 7539230 pairs aligned concordantly 0 times; of these: 2143915 (28.44%) aligned discordantly 1 time ---- 5395315 pairs aligned 0 times concordantly or discordantly; of these: 10790630 mates make up the pairs; of these: 9805866 (90.87%) aligned 0 times 501118 (4.64%) aligned exactly 1 time 483646 (4.48%) aligned >1 times 65.36% overall alignment rate Time searching: 00:28:44 Overall time: 00:28:44 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] 1046435 / 8733666 = 0.1198 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 17:15:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.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 17:15:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:15:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:15:56: 1000000 INFO @ Wed, 08 Dec 2021 17:16:06: 2000000 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 17:16:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.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 17:16:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:16:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:16:16: 3000000 INFO @ Wed, 08 Dec 2021 17:16:27: 4000000 INFO @ Wed, 08 Dec 2021 17:16:27: 1000000 INFO @ Wed, 08 Dec 2021 17:16:37: 5000000 INFO @ Wed, 08 Dec 2021 17:16:39: 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 17:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.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 17:16:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:16:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:16:48: 6000000 INFO @ Wed, 08 Dec 2021 17:16:51: 3000000 INFO @ Wed, 08 Dec 2021 17:16:58: 1000000 INFO @ Wed, 08 Dec 2021 17:16:59: 7000000 INFO @ Wed, 08 Dec 2021 17:17:03: 4000000 INFO @ Wed, 08 Dec 2021 17:17:09: 8000000 INFO @ Wed, 08 Dec 2021 17:17:10: 2000000 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: 3000000 INFO @ Wed, 08 Dec 2021 17:17:26: 6000000 INFO @ Wed, 08 Dec 2021 17:17:31: 10000000 INFO @ Wed, 08 Dec 2021 17:17:34: 4000000 INFO @ Wed, 08 Dec 2021 17:17:39: 7000000 INFO @ Wed, 08 Dec 2021 17:17:41: 11000000 INFO @ Wed, 08 Dec 2021 17:17:46: 5000000 INFO @ Wed, 08 Dec 2021 17:17:51: 8000000 INFO @ Wed, 08 Dec 2021 17:17:52: 12000000 INFO @ Wed, 08 Dec 2021 17:17:59: 6000000 INFO @ Wed, 08 Dec 2021 17:18:02: 13000000 INFO @ Wed, 08 Dec 2021 17:18:03: 9000000 INFO @ Wed, 08 Dec 2021 17:18:12: 7000000 INFO @ Wed, 08 Dec 2021 17:18:12: 14000000 INFO @ Wed, 08 Dec 2021 17:18:16: 10000000 INFO @ Wed, 08 Dec 2021 17:18:23: 15000000 INFO @ Wed, 08 Dec 2021 17:18:25: 8000000 INFO @ Wed, 08 Dec 2021 17:18:29: 11000000 INFO @ Wed, 08 Dec 2021 17:18:33: 16000000 INFO @ Wed, 08 Dec 2021 17:18:36: 9000000 INFO @ Wed, 08 Dec 2021 17:18:38: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:18:38: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:18:38: #1 total tags in treatment: 5765499 INFO @ Wed, 08 Dec 2021 17:18:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:18:38: #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 17:18:38: #1 tags after filtering in treatment: 5320487 INFO @ Wed, 08 Dec 2021 17:18:38: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:18:38: #1 finished! INFO @ Wed, 08 Dec 2021 17:18:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:18:38: #2 number of paired peaks: 601 WARNING @ Wed, 08 Dec 2021 17:18:38: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Wed, 08 Dec 2021 17:18:38: start model_add_line... INFO @ Wed, 08 Dec 2021 17:18:39: start X-correlation... INFO @ Wed, 08 Dec 2021 17:18:39: end of X-cor INFO @ Wed, 08 Dec 2021 17:18:39: #2 finished! INFO @ Wed, 08 Dec 2021 17:18:39: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 17:18:39: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 17:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.05_model.r WARNING @ Wed, 08 Dec 2021 17:18:39: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:18:39: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 17:18:39: #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 17:18:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:18:40: 12000000 INFO @ Wed, 08 Dec 2021 17:18:48: 10000000 INFO @ Wed, 08 Dec 2021 17:18:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:18:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:19:01: 11000000 INFO @ Wed, 08 Dec 2021 17:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.05_summits.bed INFO @ Wed, 08 Dec 2021 17:19:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:19:05: 14000000 INFO @ Wed, 08 Dec 2021 17:19:13: 12000000 INFO @ Wed, 08 Dec 2021 17:19:17: 15000000 INFO @ Wed, 08 Dec 2021 17:19:26: 13000000 INFO @ Wed, 08 Dec 2021 17:19:30: 16000000 INFO @ Wed, 08 Dec 2021 17:19:35: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:19:35: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:19:35: #1 total tags in treatment: 5765499 INFO @ Wed, 08 Dec 2021 17:19:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:19:35: #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 17:19:35: #1 tags after filtering in treatment: 5320487 INFO @ Wed, 08 Dec 2021 17:19:35: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:19:35: #1 finished! INFO @ Wed, 08 Dec 2021 17:19:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:19:36: #2 number of paired peaks: 601 WARNING @ Wed, 08 Dec 2021 17:19:36: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Wed, 08 Dec 2021 17:19:36: start model_add_line... INFO @ Wed, 08 Dec 2021 17:19:36: start X-correlation... INFO @ Wed, 08 Dec 2021 17:19:36: end of X-cor INFO @ Wed, 08 Dec 2021 17:19:36: #2 finished! INFO @ Wed, 08 Dec 2021 17:19:36: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 17:19:36: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 17:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.10_model.r WARNING @ Wed, 08 Dec 2021 17:19:37: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:19:37: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 17:19:37: #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 17:19:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:19:38: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:19:49: 15000000 INFO @ Wed, 08 Dec 2021 17:19:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:20:00: 16000000 INFO @ Wed, 08 Dec 2021 17:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.10_summits.bed INFO @ Wed, 08 Dec 2021 17:20:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:20:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:20:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:20:05: #1 total tags in treatment: 5765499 INFO @ Wed, 08 Dec 2021 17:20:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:20:05: #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 17:20:05: #1 tags after filtering in treatment: 5320487 INFO @ Wed, 08 Dec 2021 17:20:05: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:20:05: #1 finished! INFO @ Wed, 08 Dec 2021 17:20:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:20:05: #2 number of paired peaks: 601 WARNING @ Wed, 08 Dec 2021 17:20:05: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Wed, 08 Dec 2021 17:20:05: start model_add_line... INFO @ Wed, 08 Dec 2021 17:20:05: start X-correlation... INFO @ Wed, 08 Dec 2021 17:20:05: end of X-cor INFO @ Wed, 08 Dec 2021 17:20:05: #2 finished! INFO @ Wed, 08 Dec 2021 17:20:05: #2 predicted fragment length is 220 bps INFO @ Wed, 08 Dec 2021 17:20:05: #2 alternative fragment length(s) may be 220 bps INFO @ Wed, 08 Dec 2021 17:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.20_model.r WARNING @ Wed, 08 Dec 2021 17:20:05: #2 Since the d (220) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:20:05: #2 You may need to consider one of the other alternative d(s): 220 WARNING @ Wed, 08 Dec 2021 17:20:05: #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 17:20:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:20:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:20:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:20:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641176/SRX10641176.20_summits.bed INFO @ Wed, 08 Dec 2021 17:20:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 2 millis CompletedMACS2peakCalling