[2024-01-25 19:51:35,656] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:35,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:35,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference
[2024-01-25 19:51:36,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:36,835] [INFO] Task started: Prodigal
[2024-01-25 19:51:36,835] [INFO] Running command: gunzip -c /var/lib/cwl/stgb16729e2-01f4-44a8-89bd-f9ac64b6356e/GCF_003030465.1_ASM303046v1_genomic.fna.gz | prodigal -d GCF_003030465.1_ASM303046v1_genomic.fna/cds.fna -a GCF_003030465.1_ASM303046v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:46,886] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:46,886] [INFO] Task started: HMMsearch
[2024-01-25 19:51:46,886] [INFO] Running command: hmmsearch --tblout GCF_003030465.1_ASM303046v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference/reference_markers.hmm GCF_003030465.1_ASM303046v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:47,111] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:47,112] [INFO] Found 6/6 markers.
[2024-01-25 19:51:47,140] [INFO] Query marker FASTA was written to GCF_003030465.1_ASM303046v1_genomic.fna/markers.fasta
[2024-01-25 19:51:47,140] [INFO] Task started: Blastn
[2024-01-25 19:51:47,141] [INFO] Running command: blastn -query GCF_003030465.1_ASM303046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference/reference_markers.fasta -out GCF_003030465.1_ASM303046v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:47,998] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:48,001] [INFO] Selected 14 target genomes.
[2024-01-25 19:51:48,001] [INFO] Target genome list was writen to GCF_003030465.1_ASM303046v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:48,018] [INFO] Task started: fastANI
[2024-01-25 19:51:48,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgb16729e2-01f4-44a8-89bd-f9ac64b6356e/GCF_003030465.1_ASM303046v1_genomic.fna.gz --refList GCF_003030465.1_ASM303046v1_genomic.fna/target_genomes.txt --output GCF_003030465.1_ASM303046v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:52:00,531] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:00,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:52:00,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:52:00,541] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:52:00,541] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:52:00,541] [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 aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	100.0	1233	1236	95	conclusive
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	93.392	957	1236	95	below_threshold
Thauera chlorobenzoica	strain=3CB1	GCA_001922305.1	96773	96773	type	True	93.3767	987	1236	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	84.9398	674	1236	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	84.365	682	1236	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	83.4093	652	1236	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	83.2522	638	1236	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	82.9246	567	1236	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	82.7672	615	1236	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	80.9606	601	1236	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	80.7165	582	1236	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	80.556	559	1236	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	79.5752	441	1236	95	below_threshold
Nitrogeniibacter aestuarii	strain=H1-1-2A	GCA_017309585.1	2815343	2815343	type	True	78.4057	294	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:52:00,545] [INFO] DFAST Taxonomy check result was written to GCF_003030465.1_ASM303046v1_genomic.fna/tc_result.tsv
[2024-01-25 19:52:00,545] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:52:00,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:52:00,546] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference/checkm_data
[2024-01-25 19:52:00,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:52:00,586] [INFO] Task started: CheckM
[2024-01-25 19:52:00,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003030465.1_ASM303046v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003030465.1_ASM303046v1_genomic.fna/checkm_input GCF_003030465.1_ASM303046v1_genomic.fna/checkm_result
[2024-01-25 19:52:42,032] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:42,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:42,047] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:42,048] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:42,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003030465.1_ASM303046v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:42,049] [INFO] Task started: Blastn
[2024-01-25 19:52:42,049] [INFO] Running command: blastn -query GCF_003030465.1_ASM303046v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d7289b9-b54d-4998-b13a-cb4bb249808e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003030465.1_ASM303046v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:43,685] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:43,687] [INFO] Selected 15 target genomes.
[2024-01-25 19:52:43,687] [INFO] Target genome list was writen to GCF_003030465.1_ASM303046v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:43,700] [INFO] Task started: fastANI
[2024-01-25 19:52:43,700] [INFO] Running command: fastANI --query /var/lib/cwl/stgb16729e2-01f4-44a8-89bd-f9ac64b6356e/GCF_003030465.1_ASM303046v1_genomic.fna.gz --refList GCF_003030465.1_ASM303046v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003030465.1_ASM303046v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:56,035] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:56,045] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:56,045] [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
GCF_003030465.1	s__Thauera aromatica	100.0	1234	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001922305.1	s__Thauera chlorobenzoica	93.3638	987	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCF_000310225.1	s__Thauera phenylacetica	84.888	680	1236	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	84.4053	677	1236	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	84.3213	685	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.62	98.32	0.86	0.80	8	-
GCA_017997795.1	s__Thauera sp017997795	84.2891	494	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422685.1	s__Thauera sp002422685	83.8194	598	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003446655.1	s__Thauera sp003446655	83.4081	486	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.50	99.50	0.90	0.90	2	-
GCF_001591165.1	s__Thauera butanivorans	83.2539	637	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790365.1	s__Thauera sp016790365	83.0511	488	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000310145.2	s__Thauera sp000310145	82.9296	613	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	98.71	98.54	0.88	0.86	4	-
GCF_000310205.1	s__Thauera linaloolentis	82.9053	569	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004295105.1	s__Thauera sp004295105	82.3849	523	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240585.1	s__Thauera sp018240585	82.3696	486	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	82.2802	584	1236	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:56,048] [INFO] GTDB search result was written to GCF_003030465.1_ASM303046v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:56,049] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:56,052] [INFO] DFAST_QC result json was written to GCF_003030465.1_ASM303046v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:56,052] [INFO] DFAST_QC completed!
[2024-01-25 19:52:56,052] [INFO] Total running time: 0h1m20s