[2023-06-29 14:42:26,894] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:42:26,898] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:42:26,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference
[2023-06-29 14:42:28,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:42:28,135] [INFO] Task started: Prodigal
[2023-06-29 14:42:28,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg53d68195-9aae-4b29-83ac-77a8e0df2b12/GCA_021629205.1_ASM2162920v1_genomic.fna.gz | prodigal -d GCA_021629205.1_ASM2162920v1_genomic.fna/cds.fna -a GCA_021629205.1_ASM2162920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:42:34,844] [INFO] Task succeeded: Prodigal
[2023-06-29 14:42:34,844] [INFO] Task started: HMMsearch
[2023-06-29 14:42:34,845] [INFO] Running command: hmmsearch --tblout GCA_021629205.1_ASM2162920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference/reference_markers.hmm GCA_021629205.1_ASM2162920v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:42:35,117] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:42:35,118] [INFO] Found 6/6 markers.
[2023-06-29 14:42:35,148] [INFO] Query marker FASTA was written to GCA_021629205.1_ASM2162920v1_genomic.fna/markers.fasta
[2023-06-29 14:42:35,149] [INFO] Task started: Blastn
[2023-06-29 14:42:35,149] [INFO] Running command: blastn -query GCA_021629205.1_ASM2162920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference/reference_markers.fasta -out GCA_021629205.1_ASM2162920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:42:35,805] [INFO] Task succeeded: Blastn
[2023-06-29 14:42:35,809] [INFO] Selected 27 target genomes.
[2023-06-29 14:42:35,809] [INFO] Target genome list was writen to GCA_021629205.1_ASM2162920v1_genomic.fna/target_genomes.txt
[2023-06-29 14:42:35,811] [INFO] Task started: fastANI
[2023-06-29 14:42:35,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d68195-9aae-4b29-83ac-77a8e0df2b12/GCA_021629205.1_ASM2162920v1_genomic.fna.gz --refList GCA_021629205.1_ASM2162920v1_genomic.fna/target_genomes.txt --output GCA_021629205.1_ASM2162920v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:42:52,661] [INFO] Task succeeded: fastANI
[2023-06-29 14:42:52,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:42:52,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:42:52,677] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:42:52,677] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:42:52,677] [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
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	79.2538	51	917	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	79.0559	84	917	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.214	74	917	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	78.1302	68	917	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.9611	61	917	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.9002	104	917	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.8814	101	917	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	76.8717	60	917	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.8333	114	917	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	76.6509	84	917	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.5889	82	917	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	76.587	51	917	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	76.5106	54	917	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:42:52,680] [INFO] DFAST Taxonomy check result was written to GCA_021629205.1_ASM2162920v1_genomic.fna/tc_result.tsv
[2023-06-29 14:42:52,681] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:42:52,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:42:52,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference/checkm_data
[2023-06-29 14:42:52,683] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:42:52,719] [INFO] Task started: CheckM
[2023-06-29 14:42:52,719] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021629205.1_ASM2162920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021629205.1_ASM2162920v1_genomic.fna/checkm_input GCA_021629205.1_ASM2162920v1_genomic.fna/checkm_result
[2023-06-29 14:43:19,424] [INFO] Task succeeded: CheckM
[2023-06-29 14:43:19,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:43:19,444] [INFO] ===== Completeness check finished =====
[2023-06-29 14:43:19,444] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:43:19,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021629205.1_ASM2162920v1_genomic.fna/markers.fasta)
[2023-06-29 14:43:19,445] [INFO] Task started: Blastn
[2023-06-29 14:43:19,445] [INFO] Running command: blastn -query GCA_021629205.1_ASM2162920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21659302-9e6e-43e0-ac6b-b940f95b81d0/dqc_reference/reference_markers_gtdb.fasta -out GCA_021629205.1_ASM2162920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:43:20,511] [INFO] Task succeeded: Blastn
[2023-06-29 14:43:20,516] [INFO] Selected 18 target genomes.
[2023-06-29 14:43:20,516] [INFO] Target genome list was writen to GCA_021629205.1_ASM2162920v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:43:20,523] [INFO] Task started: fastANI
[2023-06-29 14:43:20,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg53d68195-9aae-4b29-83ac-77a8e0df2b12/GCA_021629205.1_ASM2162920v1_genomic.fna.gz --refList GCA_021629205.1_ASM2162920v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021629205.1_ASM2162920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:43:29,917] [INFO] Task succeeded: fastANI
[2023-06-29 14:43:29,935] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:43:29,936] [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_003490145.1	s__CAG-95 sp900066375	98.5988	816	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.74	97.55	0.91	0.82	5	conclusive
GCA_902766365.1	s__CAG-95 sp902766365	90.3717	644	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622575.1	s__CAG-95 sp017622575	78.5979	296	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438155.1	s__CAG-95 sp000438155	78.541	217	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.06	97.32	0.83	0.81	5	-
GCA_000436115.1	s__CAG-95 sp000436115	78.4396	244	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.37	99.32	0.91	0.90	3	-
GCA_014803415.1	s__CAG-95 sp014803415	78.2036	223	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	97.80	97.80	0.82	0.82	2	-
GCA_900553305.1	s__CAG-95 sp900553305	78.1873	156	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	99.81	99.81	0.85	0.85	2	-
GCA_018384375.1	s__CAG-95 sp018384375	77.9621	224	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.73	98.22	0.80	0.77	3	-
GCA_017411305.1	s__CAG-95 sp017411305	77.6233	170	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621815.1	s__CAG-95 sp017621815	77.6013	218	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000403495.2	s__CAG-95 sp000403495	77.4233	145	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	98.68	98.68	0.87	0.87	2	-
GCA_014804785.1	s__CAG-95 sp014804785	77.2225	172	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057005.1	s__Acetatifactor sp015057005	77.1653	71	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465845.1	s__Acetatifactor sp017465845	76.9424	91	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695765.1	s__VUNI01 sp009695765	76.8717	60	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017476765.1	s__RGIG3040 sp017476765	76.452	56	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:43:29,938] [INFO] GTDB search result was written to GCA_021629205.1_ASM2162920v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:43:29,938] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:43:29,943] [INFO] DFAST_QC result json was written to GCA_021629205.1_ASM2162920v1_genomic.fna/dqc_result.json
[2023-06-29 14:43:29,943] [INFO] DFAST_QC completed!
[2023-06-29 14:43:29,944] [INFO] Total running time: 0h1m3s