[2023-06-29 14:56:12,474] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:56:12,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:56:12,477] [INFO] DQC Reference Directory: /var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference
[2023-06-29 14:56:13,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:56:13,720] [INFO] Task started: Prodigal
[2023-06-29 14:56:13,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg68103338-c910-4195-8230-9bcecf83c3ce/GCA_021780495.1_ASM2178049v1_genomic.fna.gz | prodigal -d GCA_021780495.1_ASM2178049v1_genomic.fna/cds.fna -a GCA_021780495.1_ASM2178049v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:56:23,935] [INFO] Task succeeded: Prodigal
[2023-06-29 14:56:23,936] [INFO] Task started: HMMsearch
[2023-06-29 14:56:23,936] [INFO] Running command: hmmsearch --tblout GCA_021780495.1_ASM2178049v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference/reference_markers.hmm GCA_021780495.1_ASM2178049v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:56:24,205] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:56:24,207] [INFO] Found 6/6 markers.
[2023-06-29 14:56:24,245] [INFO] Query marker FASTA was written to GCA_021780495.1_ASM2178049v1_genomic.fna/markers.fasta
[2023-06-29 14:56:24,246] [INFO] Task started: Blastn
[2023-06-29 14:56:24,246] [INFO] Running command: blastn -query GCA_021780495.1_ASM2178049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference/reference_markers.fasta -out GCA_021780495.1_ASM2178049v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:56:24,904] [INFO] Task succeeded: Blastn
[2023-06-29 14:56:24,909] [INFO] Selected 13 target genomes.
[2023-06-29 14:56:24,910] [INFO] Target genome list was writen to GCA_021780495.1_ASM2178049v1_genomic.fna/target_genomes.txt
[2023-06-29 14:56:24,912] [INFO] Task started: fastANI
[2023-06-29 14:56:24,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg68103338-c910-4195-8230-9bcecf83c3ce/GCA_021780495.1_ASM2178049v1_genomic.fna.gz --refList GCA_021780495.1_ASM2178049v1_genomic.fna/target_genomes.txt --output GCA_021780495.1_ASM2178049v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:56:34,235] [INFO] Task succeeded: fastANI
[2023-06-29 14:56:34,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:56:34,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:56:34,242] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:56:34,242] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:56:34,242] [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
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	78.3588	296	1190	95	below_threshold
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	78.2649	293	1190	95	below_threshold
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	78.2293	293	1190	95	below_threshold
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	77.8991	232	1190	95	below_threshold
Geobacter chapellei	strain=DSM 13688	GCA_018531195.1	44671	44671	type	True	76.9856	149	1190	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:56:34,244] [INFO] DFAST Taxonomy check result was written to GCA_021780495.1_ASM2178049v1_genomic.fna/tc_result.tsv
[2023-06-29 14:56:34,245] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:56:34,245] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:56:34,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference/checkm_data
[2023-06-29 14:56:34,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:56:34,290] [INFO] Task started: CheckM
[2023-06-29 14:56:34,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021780495.1_ASM2178049v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021780495.1_ASM2178049v1_genomic.fna/checkm_input GCA_021780495.1_ASM2178049v1_genomic.fna/checkm_result
[2023-06-29 14:57:08,905] [INFO] Task succeeded: CheckM
[2023-06-29 14:57:08,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:57:08,930] [INFO] ===== Completeness check finished =====
[2023-06-29 14:57:08,931] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:57:08,931] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021780495.1_ASM2178049v1_genomic.fna/markers.fasta)
[2023-06-29 14:57:08,932] [INFO] Task started: Blastn
[2023-06-29 14:57:08,932] [INFO] Running command: blastn -query GCA_021780495.1_ASM2178049v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66fc5d85-1b42-4ab9-afe8-213909a6310d/dqc_reference/reference_markers_gtdb.fasta -out GCA_021780495.1_ASM2178049v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:57:09,861] [INFO] Task succeeded: Blastn
[2023-06-29 14:57:09,866] [INFO] Selected 19 target genomes.
[2023-06-29 14:57:09,867] [INFO] Target genome list was writen to GCA_021780495.1_ASM2178049v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:57:09,894] [INFO] Task started: fastANI
[2023-06-29 14:57:09,894] [INFO] Running command: fastANI --query /var/lib/cwl/stg68103338-c910-4195-8230-9bcecf83c3ce/GCA_021780495.1_ASM2178049v1_genomic.fna.gz --refList GCA_021780495.1_ASM2178049v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021780495.1_ASM2178049v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:57:22,149] [INFO] Task succeeded: fastANI
[2023-06-29 14:57:22,170] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 14:57:22,170] [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_016650295.1	s__CAIPTY01 sp016650295	79.7261	456	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720395.1	s__CAIPTY01 sp016720395	79.5629	417	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298925.1	s__Pelotalea sp002298925	78.8699	332	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015688915.1	s__JACPFJ01 sp015688915	78.5821	245	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380135.1	s__JACRCG01 sp014380135	78.5287	233	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802355.1	s__Oryzomonas sagensis	78.372	295	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001802125.1	s__JACRCG01 sp001802125	78.3589	310	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.79	99.67	0.87	0.84	4	-
GCA_016182975.1	s__JACPFJ01 sp016182975	78.3127	233	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802365.1	s__Oryzomonas japonica	78.2776	292	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	96.07	96.07	0.87	0.87	2	-
GCF_016865365.1	s__Pelotalea sp012556225	78.2713	289	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	99.99	99.99	1.00	1.00	2	-
GCA_903868145.1	s__CAIPTY01 sp903868145	78.0101	285	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	99.88	99.88	0.95	0.95	2	-
GCF_000015045.1	s__Pseudopelobacter propionicus	77.9642	227	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219145.1	s__JACRCG01 sp016219145	77.8426	180	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377095.1	s__Pseudopelobacter sp013377095	77.5432	245	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862245.1	s__JACRCG01 sp903862245	77.2282	173	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.89	99.85	0.93	0.90	4	-
GCA_002423105.1	s__Trichlorobacter sp002423105	77.0011	146	1190	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	76.9477	149	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	99.58	99.35	0.95	0.91	3	-
GCA_903901875.1	s__JACRCG01 sp903901875	76.8857	114	1190	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	99.81	99.81	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:57:22,172] [INFO] GTDB search result was written to GCA_021780495.1_ASM2178049v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:57:22,173] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:57:22,177] [INFO] DFAST_QC result json was written to GCA_021780495.1_ASM2178049v1_genomic.fna/dqc_result.json
[2023-06-29 14:57:22,177] [INFO] DFAST_QC completed!
[2023-06-29 14:57:22,177] [INFO] Total running time: 0h1m10s