[2023-06-30 20:38:29,833] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:38:29,836] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:38:29,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference
[2023-06-30 20:38:31,010] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:38:31,011] [INFO] Task started: Prodigal
[2023-06-30 20:38:31,011] [INFO] Running command: gunzip -c /var/lib/cwl/stgee9be186-17fc-4c16-b960-85a8c60d3c4f/GCA_016939035.1_ASM1693903v1_genomic.fna.gz | prodigal -d GCA_016939035.1_ASM1693903v1_genomic.fna/cds.fna -a GCA_016939035.1_ASM1693903v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:38:49,817] [INFO] Task succeeded: Prodigal
[2023-06-30 20:38:49,817] [INFO] Task started: HMMsearch
[2023-06-30 20:38:49,818] [INFO] Running command: hmmsearch --tblout GCA_016939035.1_ASM1693903v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference/reference_markers.hmm GCA_016939035.1_ASM1693903v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:38:50,015] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:38:50,016] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgee9be186-17fc-4c16-b960-85a8c60d3c4f/GCA_016939035.1_ASM1693903v1_genomic.fna.gz]
[2023-06-30 20:38:50,048] [INFO] Query marker FASTA was written to GCA_016939035.1_ASM1693903v1_genomic.fna/markers.fasta
[2023-06-30 20:38:50,049] [INFO] Task started: Blastn
[2023-06-30 20:38:50,049] [INFO] Running command: blastn -query GCA_016939035.1_ASM1693903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference/reference_markers.fasta -out GCA_016939035.1_ASM1693903v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:38:50,549] [INFO] Task succeeded: Blastn
[2023-06-30 20:38:50,552] [INFO] Selected 12 target genomes.
[2023-06-30 20:38:50,553] [INFO] Target genome list was writen to GCA_016939035.1_ASM1693903v1_genomic.fna/target_genomes.txt
[2023-06-30 20:38:50,554] [INFO] Task started: fastANI
[2023-06-30 20:38:50,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgee9be186-17fc-4c16-b960-85a8c60d3c4f/GCA_016939035.1_ASM1693903v1_genomic.fna.gz --refList GCA_016939035.1_ASM1693903v1_genomic.fna/target_genomes.txt --output GCA_016939035.1_ASM1693903v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:38:56,967] [INFO] Task succeeded: fastANI
[2023-06-30 20:38:56,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:38:56,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:38:56,978] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:38:56,978] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:38:56,978] [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
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	94.9465	436	822	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	94.7816	448	822	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	94.6488	452	822	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	82.7797	324	822	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.3139	100	822	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.938	68	822	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.4825	56	822	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.2817	64	822	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.2795	66	822	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:38:56,980] [INFO] DFAST Taxonomy check result was written to GCA_016939035.1_ASM1693903v1_genomic.fna/tc_result.tsv
[2023-06-30 20:38:56,981] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:38:56,981] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:38:56,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference/checkm_data
[2023-06-30 20:38:56,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:38:57,021] [INFO] Task started: CheckM
[2023-06-30 20:38:57,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016939035.1_ASM1693903v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016939035.1_ASM1693903v1_genomic.fna/checkm_input GCA_016939035.1_ASM1693903v1_genomic.fna/checkm_result
[2023-06-30 20:39:52,354] [INFO] Task succeeded: CheckM
[2023-06-30 20:39:52,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 49.31%
Contamintation: 14.35%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 20:39:52,378] [INFO] ===== Completeness check finished =====
[2023-06-30 20:39:52,378] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:39:52,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016939035.1_ASM1693903v1_genomic.fna/markers.fasta)
[2023-06-30 20:39:52,379] [INFO] Task started: Blastn
[2023-06-30 20:39:52,379] [INFO] Running command: blastn -query GCA_016939035.1_ASM1693903v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c2d8ee4-408b-401c-9b95-e963fc325b4e/dqc_reference/reference_markers_gtdb.fasta -out GCA_016939035.1_ASM1693903v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:39:52,894] [INFO] Task succeeded: Blastn
[2023-06-30 20:39:52,897] [INFO] Selected 12 target genomes.
[2023-06-30 20:39:52,898] [INFO] Target genome list was writen to GCA_016939035.1_ASM1693903v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:39:52,898] [INFO] Task started: fastANI
[2023-06-30 20:39:52,898] [INFO] Running command: fastANI --query /var/lib/cwl/stgee9be186-17fc-4c16-b960-85a8c60d3c4f/GCA_016939035.1_ASM1693903v1_genomic.fna.gz --refList GCA_016939035.1_ASM1693903v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016939035.1_ASM1693903v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:39:59,751] [INFO] Task succeeded: fastANI
[2023-06-30 20:39:59,762] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:39:59,762] [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_015074785.1	s__Prevotella sp015074785	95.1386	502	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000157935.1	s__Prevotella copri	94.8719	446	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_019127135.1	s__Prevotella sp900551275	93.2175	497	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_900557255.1	s__Prevotella sp900557255	93.1235	309	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224675.1	s__Prevotella copri_A	86.4434	388	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_900544825.1	s__Prevotella sp900544825	86.2393	379	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_019249655.1	s__Prevotella sp900767615	85.7175	443	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCA_900551985.1	s__Prevotella sp900551985	85.5538	364	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_900557035.1	s__Prevotella sp900557035	84.964	290	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900556795.1	s__Prevotella sp900556795	84.3991	260	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
GCA_900555035.1	s__Prevotella sp900555035	84.2702	360	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765465.1	s__Prevotella sp900765465	83.4361	224	822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:39:59,764] [INFO] GTDB search result was written to GCA_016939035.1_ASM1693903v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:39:59,765] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:39:59,768] [INFO] DFAST_QC result json was written to GCA_016939035.1_ASM1693903v1_genomic.fna/dqc_result.json
[2023-06-30 20:39:59,768] [INFO] DFAST_QC completed!
[2023-06-30 20:39:59,768] [INFO] Total running time: 0h1m30s