[2024-01-24 14:12:16,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:16,247] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:16,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference
[2024-01-24 14:12:17,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:17,542] [INFO] Task started: Prodigal
[2024-01-24 14:12:17,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg5965b243-fb27-4e22-be50-d9ed85da9a9b/GCF_002959615.1_ASM295961v1_genomic.fna.gz | prodigal -d GCF_002959615.1_ASM295961v1_genomic.fna/cds.fna -a GCF_002959615.1_ASM295961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:27,576] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:27,577] [INFO] Task started: HMMsearch
[2024-01-24 14:12:27,577] [INFO] Running command: hmmsearch --tblout GCF_002959615.1_ASM295961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference/reference_markers.hmm GCF_002959615.1_ASM295961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:27,962] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:27,963] [INFO] Found 6/6 markers.
[2024-01-24 14:12:27,997] [INFO] Query marker FASTA was written to GCF_002959615.1_ASM295961v1_genomic.fna/markers.fasta
[2024-01-24 14:12:27,998] [INFO] Task started: Blastn
[2024-01-24 14:12:27,998] [INFO] Running command: blastn -query GCF_002959615.1_ASM295961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference/reference_markers.fasta -out GCF_002959615.1_ASM295961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:28,663] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:28,671] [INFO] Selected 8 target genomes.
[2024-01-24 14:12:28,671] [INFO] Target genome list was writen to GCF_002959615.1_ASM295961v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:28,691] [INFO] Task started: fastANI
[2024-01-24 14:12:28,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg5965b243-fb27-4e22-be50-d9ed85da9a9b/GCF_002959615.1_ASM295961v1_genomic.fna.gz --refList GCF_002959615.1_ASM295961v1_genomic.fna/target_genomes.txt --output GCF_002959615.1_ASM295961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:34,889] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:34,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:34,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:34,898] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:12:34,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:34,898] [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
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	100.0	1183	1186	95	conclusive
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	99.9988	1178	1186	95	conclusive
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	99.9972	1177	1186	95	conclusive
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	99.9687	1144	1186	95	conclusive
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	99.0995	919	1186	95	conclusive
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	86.8688	169	1186	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.8898	173	1186	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.6548	62	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:34,900] [INFO] DFAST Taxonomy check result was written to GCF_002959615.1_ASM295961v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:34,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:34,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:34,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference/checkm_data
[2024-01-24 14:12:34,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:34,937] [INFO] Task started: CheckM
[2024-01-24 14:12:34,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002959615.1_ASM295961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002959615.1_ASM295961v1_genomic.fna/checkm_input GCF_002959615.1_ASM295961v1_genomic.fna/checkm_result
[2024-01-24 14:13:10,003] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:10,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:10,026] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:10,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:10,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002959615.1_ASM295961v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:10,027] [INFO] Task started: Blastn
[2024-01-24 14:13:10,027] [INFO] Running command: blastn -query GCF_002959615.1_ASM295961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc25bd24a-005b-4abb-a4b5-ceab400b97ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_002959615.1_ASM295961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:11,123] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:11,128] [INFO] Selected 17 target genomes.
[2024-01-24 14:13:11,128] [INFO] Target genome list was writen to GCF_002959615.1_ASM295961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:11,157] [INFO] Task started: fastANI
[2024-01-24 14:13:11,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg5965b243-fb27-4e22-be50-d9ed85da9a9b/GCF_002959615.1_ASM295961v1_genomic.fna.gz --refList GCF_002959615.1_ASM295961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002959615.1_ASM295961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:20,044] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:20,060] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:20,060] [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_008121495.1	s__Ruminococcus_B gnavus	99.9989	1176	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	conclusive
GCA_900544395.1	s__Ruminococcus_B sp900544395	85.3697	614	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
GCA_003480425.1	s__Schaedlerella sp900066545	80.3633	221	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCA_001312505.1	s__Mediterraneibacter faecis	79.8025	238	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_012524165.2	s__Muricomes sp012524165	79.0087	238	1186	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_000155205.1	s__Mediterraneibacter lactaris	78.9855	234	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_002320245.1	s__Schaedlerella sp002320245	78.6807	216	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	78.6038	266	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCA_905203555.1	s__Schaedlerella sp905203555	78.3475	201	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	77.6132	135	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	77.4447	167	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCF_004346165.1	s__Muricomes intestini	77.3457	163	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.31	99.22	0.86	0.79	6	-
GCA_904418845.1	s__Mediterraneibacter sp904418845	77.0794	167	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	76.9297	150	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_019115385.1	s__Mediterraneibacter avicola	76.9212	150	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.73	98.73	0.86	0.86	2	-
GCA_019119675.1	s__Mediterraneibacter faecipullorum	76.907	157	1186	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:20,062] [INFO] GTDB search result was written to GCF_002959615.1_ASM295961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:20,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:20,066] [INFO] DFAST_QC result json was written to GCF_002959615.1_ASM295961v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:20,066] [INFO] DFAST_QC completed!
[2024-01-24 14:13:20,066] [INFO] Total running time: 0h1m4s