[2023-03-15 22:10:43,682] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:10:43,683] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:10:43,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference
[2023-03-15 22:10:44,777] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:10:44,777] [INFO] Task started: Prodigal
[2023-03-15 22:10:44,778] [INFO] Running command: cat /var/lib/cwl/stgfedb5f6d-65d0-4435-bb7e-bf4655f935c2/OceanDNA-b34127.fa | prodigal -d OceanDNA-b34127/cds.fna -a OceanDNA-b34127/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:11:02,915] [INFO] Task succeeded: Prodigal
[2023-03-15 22:11:02,916] [INFO] Task started: HMMsearch
[2023-03-15 22:11:02,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b34127/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference/reference_markers.hmm OceanDNA-b34127/protein.faa > /dev/null
[2023-03-15 22:11:03,131] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:11:03,132] [INFO] Found 6/6 markers.
[2023-03-15 22:11:03,150] [INFO] Query marker FASTA was written to OceanDNA-b34127/markers.fasta
[2023-03-15 22:11:03,151] [INFO] Task started: Blastn
[2023-03-15 22:11:03,151] [INFO] Running command: blastn -query OceanDNA-b34127/markers.fasta -db /var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference/reference_markers.fasta -out OceanDNA-b34127/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:11:04,098] [INFO] Task succeeded: Blastn
[2023-03-15 22:11:04,100] [INFO] Selected 18 target genomes.
[2023-03-15 22:11:04,100] [INFO] Target genome list was writen to OceanDNA-b34127/target_genomes.txt
[2023-03-15 22:11:04,109] [INFO] Task started: fastANI
[2023-03-15 22:11:04,109] [INFO] Running command: fastANI --query /var/lib/cwl/stgfedb5f6d-65d0-4435-bb7e-bf4655f935c2/OceanDNA-b34127.fa --refList OceanDNA-b34127/target_genomes.txt --output OceanDNA-b34127/fastani_result.tsv --threads 1
[2023-03-15 22:11:16,807] [INFO] Task succeeded: fastANI
[2023-03-15 22:11:16,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:11:16,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:11:16,818] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:11:16,819] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:11:16,819] [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
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.8766	381	940	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	79.5899	368	940	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	79.5387	413	940	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.4629	376	940	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	79.4208	386	940	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	79.3959	364	940	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	79.3924	368	940	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	79.3872	373	940	95	below_threshold
Aromatoleum toluvorans	strain=Td21	GCA_012910905.1	92002	92002	type	True	79.2904	376	940	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	79.265	351	940	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	79.2295	367	940	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	79.2239	376	940	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	79.0931	376	940	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.6554	307	940	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.6088	344	940	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	78.588	319	940	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	78.5459	305	940	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	77.3388	236	940	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:11:16,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34127/tc_result.tsv
[2023-03-15 22:11:16,819] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:11:16,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:11:16,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference/checkm_data
[2023-03-15 22:11:16,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:11:16,824] [INFO] Task started: CheckM
[2023-03-15 22:11:16,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34127/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34127/checkm_input OceanDNA-b34127/checkm_result
[2023-03-15 22:12:06,203] [INFO] Task succeeded: CheckM
[2023-03-15 22:12:06,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:12:06,206] [INFO] ===== Completeness check finished =====
[2023-03-15 22:12:06,206] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:12:06,206] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34127/markers.fasta)
[2023-03-15 22:12:06,207] [INFO] Task started: Blastn
[2023-03-15 22:12:06,207] [INFO] Running command: blastn -query OceanDNA-b34127/markers.fasta -db /var/lib/cwl/stg57fc13bb-a76f-4c47-8703-8522ba12564f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34127/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:12:08,140] [INFO] Task succeeded: Blastn
[2023-03-15 22:12:08,141] [INFO] Selected 17 target genomes.
[2023-03-15 22:12:08,141] [INFO] Target genome list was writen to OceanDNA-b34127/target_genomes_gtdb.txt
[2023-03-15 22:12:08,283] [INFO] Task started: fastANI
[2023-03-15 22:12:08,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgfedb5f6d-65d0-4435-bb7e-bf4655f935c2/OceanDNA-b34127.fa --refList OceanDNA-b34127/target_genomes_gtdb.txt --output OceanDNA-b34127/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:12:21,327] [INFO] Task succeeded: fastANI
[2023-03-15 22:12:21,337] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:12:21,337] [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_013911595.1	s__Azoarcus_D sp013911595	93.343	619	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002872475.1	s__Azoarcus_D pumilus	91.3719	769	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310225.1	s__Thauera phenylacetica	79.8768	381	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963015.1	s__Thauera sp003963015	79.712	377	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310185.1	s__Thauera aminoaromatica	79.5737	370	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCF_001591165.1	s__Thauera butanivorans	79.4368	378	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001051995.2	s__Thauera humireducens	79.4268	385	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.91	97.91	0.83	0.83	2	-
GCF_012910905.1	s__Aromatoleum toluvorans	79.2526	378	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	79.2242	376	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCF_003628555.1	s__Aromatoleum sp003628555	79.1839	360	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910805.1	s__Aromatoleum evansii	79.1378	373	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	79.1128	383	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240785.1	s__Thauera sp018240785	79.1027	372	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911005.1	s__Aromatoleum toluolicum	79.0697	378	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014822185.1	s__Aromatoleum sp014822185	79.0139	379	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001274695.1	s__Aromatoleum sp001274695	78.5878	333	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Aromatoleum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910885.1	s__Azoarcus_F taiwanensis	78.2911	306	940	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:12:21,338] [INFO] GTDB search result was written to OceanDNA-b34127/result_gtdb.tsv
[2023-03-15 22:12:21,338] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:12:21,340] [INFO] DFAST_QC result json was written to OceanDNA-b34127/dqc_result.json
[2023-03-15 22:12:21,340] [INFO] DFAST_QC completed!
[2023-03-15 22:12:21,340] [INFO] Total running time: 0h1m38s