[2023-03-15 15:51:29,975] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,975] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,975] [INFO] DQC Reference Directory: /var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference
[2023-03-15 15:51:31,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,680] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,680] [INFO] Running command: cat /var/lib/cwl/stga137b354-307c-491f-b82b-719c3dc63a52/OceanDNA-b10707.fa | prodigal -d OceanDNA-b10707/cds.fna -a OceanDNA-b10707/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:46,492] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:46,492] [INFO] Task started: HMMsearch
[2023-03-15 15:51:46,492] [INFO] Running command: hmmsearch --tblout OceanDNA-b10707/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference/reference_markers.hmm OceanDNA-b10707/protein.faa > /dev/null
[2023-03-15 15:51:46,675] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:46,676] [INFO] Found 6/6 markers.
[2023-03-15 15:51:46,690] [INFO] Query marker FASTA was written to OceanDNA-b10707/markers.fasta
[2023-03-15 15:51:46,691] [INFO] Task started: Blastn
[2023-03-15 15:51:46,691] [INFO] Running command: blastn -query OceanDNA-b10707/markers.fasta -db /var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference/reference_markers.fasta -out OceanDNA-b10707/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:47,291] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:47,292] [INFO] Selected 25 target genomes.
[2023-03-15 15:51:47,292] [INFO] Target genome list was writen to OceanDNA-b10707/target_genomes.txt
[2023-03-15 15:51:47,305] [INFO] Task started: fastANI
[2023-03-15 15:51:47,305] [INFO] Running command: fastANI --query /var/lib/cwl/stga137b354-307c-491f-b82b-719c3dc63a52/OceanDNA-b10707.fa --refList OceanDNA-b10707/target_genomes.txt --output OceanDNA-b10707/fastani_result.tsv --threads 1
[2023-03-15 15:52:04,585] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:04,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:52:04,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:52:04,596] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:52:04,596] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 15:52:04,596] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.7019	161	733	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.6998	125	733	95	below_threshold
Patiriisocius marinistellae	strain=KK4	GCA_009014635.1	2494560	2494560	type	True	76.6443	127	733	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.6151	154	733	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.6116	147	733	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.5858	102	733	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.3333	109	733	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.3196	123	733	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.1097	78	733	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	75.8553	61	733	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	75.8194	69	733	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	75.7548	57	733	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	75.6314	57	733	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	75.5982	56	733	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	75.5801	57	733	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	75.5077	51	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:52:04,596] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10707/tc_result.tsv
[2023-03-15 15:52:04,596] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:52:04,596] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:52:04,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference/checkm_data
[2023-03-15 15:52:04,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:52:04,601] [INFO] Task started: CheckM
[2023-03-15 15:52:04,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10707/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10707/checkm_input OceanDNA-b10707/checkm_result
[2023-03-15 15:52:44,560] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:44,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:52:44,562] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:44,563] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:44,563] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10707/markers.fasta)
[2023-03-15 15:52:44,564] [INFO] Task started: Blastn
[2023-03-15 15:52:44,564] [INFO] Running command: blastn -query OceanDNA-b10707/markers.fasta -db /var/lib/cwl/stg167bbbe4-0899-4c68-886c-6ee8bedbd6c6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10707/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:45,401] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:45,402] [INFO] Selected 24 target genomes.
[2023-03-15 15:52:45,402] [INFO] Target genome list was writen to OceanDNA-b10707/target_genomes_gtdb.txt
[2023-03-15 15:52:45,430] [INFO] Task started: fastANI
[2023-03-15 15:52:45,430] [INFO] Running command: fastANI --query /var/lib/cwl/stga137b354-307c-491f-b82b-719c3dc63a52/OceanDNA-b10707.fa --refList OceanDNA-b10707/target_genomes_gtdb.txt --output OceanDNA-b10707/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:52:57,929] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:57,941] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:52:57,941] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_011044175.1	s__Marinirhabdus sp011044175	76.7882	133	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813135.1	s__Altibacter sp002813135	76.7273	131	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974325.1	s__Patiriisocius marinus	76.7159	124	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.7019	161	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333325.1	s__Ulvibacter_A alkanivorans	76.6978	112	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
GCA_002337605.1	s__Marinirhabdus sp002337605	76.6971	162	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_009014635.1	s__Patiriisocius marinistellae	76.6443	127	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.6116	147	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_000170815.1	s__Patiriisocius sp000170815	76.5796	101	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Patiriisocius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	76.5524	122	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCA_002364245.1	s__Marixanthomonas sp002364245	76.5236	78	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707745.1	s__Marinirhabdus sp002707745	76.403	110	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.3333	109	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	76.2609	98	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	76.2514	125	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019090365.1	s__GCA-002733185 sp019090365	76.1359	77	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018669795.1	s__GCA-002733185 sp018669795	76.129	71	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCF_001418105.1	s__Oceanihabitans himadriensis	75.8194	69	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632745.1	s__Aquimarina aggregata	75.7548	57	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCA_905181835.1	s__GCA-002733185 sp905181835	75.6068	55	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	75.5982	56	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:52:57,941] [INFO] GTDB search result was written to OceanDNA-b10707/result_gtdb.tsv
[2023-03-15 15:52:57,941] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:52:57,944] [INFO] DFAST_QC result json was written to OceanDNA-b10707/dqc_result.json
[2023-03-15 15:52:57,944] [INFO] DFAST_QC completed!
[2023-03-15 15:52:57,944] [INFO] Total running time: 0h1m28s