[2024-01-24 12:47:22,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,033] [INFO] DQC Reference Directory: /var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference
[2024-01-24 12:47:23,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,255] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,255] [INFO] Running command: gunzip -c /var/lib/cwl/stg153ea951-5083-41cd-834a-30bd07daede2/GCF_000020385.1_ASM2038v1_genomic.fna.gz | prodigal -d GCF_000020385.1_ASM2038v1_genomic.fna/cds.fna -a GCF_000020385.1_ASM2038v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:34,858] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:34,859] [INFO] Task started: HMMsearch
[2024-01-24 12:47:34,859] [INFO] Running command: hmmsearch --tblout GCF_000020385.1_ASM2038v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference/reference_markers.hmm GCF_000020385.1_ASM2038v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:35,196] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:35,197] [INFO] Found 6/6 markers.
[2024-01-24 12:47:35,235] [INFO] Query marker FASTA was written to GCF_000020385.1_ASM2038v1_genomic.fna/markers.fasta
[2024-01-24 12:47:35,236] [INFO] Task started: Blastn
[2024-01-24 12:47:35,236] [INFO] Running command: blastn -query GCF_000020385.1_ASM2038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference/reference_markers.fasta -out GCF_000020385.1_ASM2038v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:35,863] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:35,866] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:35,866] [INFO] Target genome list was writen to GCF_000020385.1_ASM2038v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:35,882] [INFO] Task started: fastANI
[2024-01-24 12:47:35,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg153ea951-5083-41cd-834a-30bd07daede2/GCF_000020385.1_ASM2038v1_genomic.fna.gz --refList GCF_000020385.1_ASM2038v1_genomic.fna/target_genomes.txt --output GCF_000020385.1_ASM2038v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:47,106] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:47,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:47,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:47,116] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:47,116] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:47,116] [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
Trichlorobacter lovleyi	strain=SZ	GCA_000020385.1	313985	313985	type	True	100.0	1330	1330	95	conclusive
Trichlorobacter thiogenes	strain=ATCC BAA-34	GCA_900167465.1	115783	115783	type	True	84.6519	811	1330	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	78.2979	190	1330	95	below_threshold
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	77.3613	200	1330	95	below_threshold
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	77.2803	210	1330	95	below_threshold
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	77.1608	201	1330	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	77.0196	131	1330	95	below_threshold
Geobacter chapellei	strain=DSM 13688	GCA_018531195.1	44671	44671	type	True	76.7679	109	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:47,118] [INFO] DFAST Taxonomy check result was written to GCF_000020385.1_ASM2038v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:47,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:47,119] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:47,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference/checkm_data
[2024-01-24 12:47:47,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:47,166] [INFO] Task started: CheckM
[2024-01-24 12:47:47,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020385.1_ASM2038v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020385.1_ASM2038v1_genomic.fna/checkm_input GCF_000020385.1_ASM2038v1_genomic.fna/checkm_result
[2024-01-24 12:48:26,107] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:26,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:26,132] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:26,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:26,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020385.1_ASM2038v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:26,134] [INFO] Task started: Blastn
[2024-01-24 12:48:26,134] [INFO] Running command: blastn -query GCF_000020385.1_ASM2038v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac027d78-6d67-4719-9eb0-e11b0e2d807f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020385.1_ASM2038v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:26,977] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:26,981] [INFO] Selected 12 target genomes.
[2024-01-24 12:48:26,981] [INFO] Target genome list was writen to GCF_000020385.1_ASM2038v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:27,003] [INFO] Task started: fastANI
[2024-01-24 12:48:27,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg153ea951-5083-41cd-834a-30bd07daede2/GCF_000020385.1_ASM2038v1_genomic.fna.gz --refList GCF_000020385.1_ASM2038v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020385.1_ASM2038v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:35,671] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:35,682] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:35,682] [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_000020385.1	s__Trichlorobacter lovleyi	100.0	1330	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167465.1	s__Trichlorobacter thiogenes	84.6399	812	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452325.1	s__Trichlorobacter sp002452325	80.6997	414	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422265.1	s__Trichlorobacter sp002422265	79.7747	431	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	97.94	97.94	0.84	0.84	2	-
GCA_002383415.1	s__Trichlorobacter sp002383415	79.0631	354	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424705.1	s__Trichlorobacter sp002424705	79.015	238	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419465.1	s__Trichlorobacter sp002419465	78.9855	402	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	99.58	99.35	0.95	0.91	3	-
GCA_002423105.1	s__Trichlorobacter sp002423105	78.5356	344	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002328035.1	s__Trichlorobacter sp002328035	77.7769	179	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802365.1	s__Oryzomonas japonica	77.1449	200	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	96.07	96.07	0.87	0.87	2	-
GCA_002322035.1	s__UBA1603 sp002322035	77.1135	132	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__UBA1603	95.0	99.35	99.35	0.84	0.84	2	-
GCA_903925005.1	s__JACRCG01 sp903925005	76.42	121	1330	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.76	99.70	0.93	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:35,684] [INFO] GTDB search result was written to GCF_000020385.1_ASM2038v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:35,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:35,689] [INFO] DFAST_QC result json was written to GCF_000020385.1_ASM2038v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:35,689] [INFO] DFAST_QC completed!
[2024-01-24 12:48:35,689] [INFO] Total running time: 0h1m14s