[2024-01-24 11:12:24,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:24,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:24,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference
[2024-01-24 11:12:27,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,094] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c7d6595-96a3-46bb-a8c7-97a6e739a41e/GCF_004346165.1_ASM434616v1_genomic.fna.gz | prodigal -d GCF_004346165.1_ASM434616v1_genomic.fna/cds.fna -a GCF_004346165.1_ASM434616v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:36,404] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:36,404] [INFO] Task started: HMMsearch
[2024-01-24 11:12:36,404] [INFO] Running command: hmmsearch --tblout GCF_004346165.1_ASM434616v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference/reference_markers.hmm GCF_004346165.1_ASM434616v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:36,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:36,764] [INFO] Found 6/6 markers.
[2024-01-24 11:12:36,799] [INFO] Query marker FASTA was written to GCF_004346165.1_ASM434616v1_genomic.fna/markers.fasta
[2024-01-24 11:12:36,799] [INFO] Task started: Blastn
[2024-01-24 11:12:36,799] [INFO] Running command: blastn -query GCF_004346165.1_ASM434616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference/reference_markers.fasta -out GCF_004346165.1_ASM434616v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:37,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:37,551] [INFO] Selected 25 target genomes.
[2024-01-24 11:12:37,551] [INFO] Target genome list was writen to GCF_004346165.1_ASM434616v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:37,585] [INFO] Task started: fastANI
[2024-01-24 11:12:37,585] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7d6595-96a3-46bb-a8c7-97a6e739a41e/GCF_004346165.1_ASM434616v1_genomic.fna.gz --refList GCF_004346165.1_ASM434616v1_genomic.fna/target_genomes.txt --output GCF_004346165.1_ASM434616v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:57,163] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:57,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:57,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:57,176] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:57,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:57,177] [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
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	100.0	1202	1204	95	conclusive
Novisyntrophococcus fermenticellae	strain=JN500902	GCA_018866245.1	2068655	2068655	type	True	81.3016	83	1204	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	78.032	256	1204	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.9515	101	1204	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	77.5939	202	1204	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.5072	155	1204	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.4117	154	1204	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	77.4047	92	1204	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.3146	153	1204	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.297	155	1204	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.1495	103	1204	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.0366	96	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:57,191] [INFO] DFAST Taxonomy check result was written to GCF_004346165.1_ASM434616v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:57,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:57,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:57,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference/checkm_data
[2024-01-24 11:12:57,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:57,234] [INFO] Task started: CheckM
[2024-01-24 11:12:57,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346165.1_ASM434616v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346165.1_ASM434616v1_genomic.fna/checkm_input GCF_004346165.1_ASM434616v1_genomic.fna/checkm_result
[2024-01-24 11:13:29,099] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:29,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:29,125] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:29,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:29,127] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346165.1_ASM434616v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:29,127] [INFO] Task started: Blastn
[2024-01-24 11:13:29,127] [INFO] Running command: blastn -query GCF_004346165.1_ASM434616v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59ca5745-44eb-48e4-b8d7-833a8f8c3e5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346165.1_ASM434616v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:30,253] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:30,258] [INFO] Selected 14 target genomes.
[2024-01-24 11:13:30,258] [INFO] Target genome list was writen to GCF_004346165.1_ASM434616v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:30,286] [INFO] Task started: fastANI
[2024-01-24 11:13:30,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c7d6595-96a3-46bb-a8c7-97a6e739a41e/GCF_004346165.1_ASM434616v1_genomic.fna.gz --refList GCF_004346165.1_ASM434616v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346165.1_ASM434616v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:41,589] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:41,615] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:41,616] [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_004346165.1	s__Muricomes intestini	100.0	1202	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.31	99.22	0.86	0.79	6	conclusive
GCF_001517425.1	s__Muricomes sp001517425	85.5488	695	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149105.1	s__Muricomes contortus_C	80.2795	548	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013911065.1	s__Muricomes sp013911065	79.6333	518	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028025.1	s__Muricomes fissicatena_A	78.441	275	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
GCA_000509105.1	s__Muricomes sp000509105	78.4189	241	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.47	98.94	0.90	0.86	4	-
GCF_003149245.1	s__Muricomes oroticus	78.2425	255	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.83	98.40	0.88	0.82	5	-
GCF_001404335.1	s__Muricomes contortus_B	78.045	268	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.80	98.64	0.86	0.83	8	-
GCF_900604355.1	s__Luxibacter massiliensis	77.6091	201	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Luxibacter	95.0	99.05	99.03	0.91	0.91	3	-
GCF_014287475.1	s__Mediterraneibacter sp014287475	77.5598	147	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.03	96.03	0.75	0.75	2	-
GCA_900765975.1	s__Schaedlerella sp900765975	77.3959	103	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_019119205.1	s__Mediterraneibacter intestinavium	76.7035	74	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.10	98.10	0.78	0.78	2	-
GCA_000403295.2	s__Schaedlerella sp000403295	76.6293	106	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
GCA_019116185.1	s__Mediterraneibacter stercorigallinarum	76.153	68	1204	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.63	98.63	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:41,619] [INFO] GTDB search result was written to GCF_004346165.1_ASM434616v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:41,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:41,626] [INFO] DFAST_QC result json was written to GCF_004346165.1_ASM434616v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:41,626] [INFO] DFAST_QC completed!
[2024-01-24 11:13:41,626] [INFO] Total running time: 0h1m17s