[2023-06-08 05:48:21,462] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:48:21,464] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:48:21,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference
[2023-06-08 05:48:23,898] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:48:23,899] [INFO] Task started: Prodigal
[2023-06-08 05:48:23,900] [INFO] Running command: gunzip -c /var/lib/cwl/stga8b89b7c-3e17-4ad6-a7ba-4be5caa92040/GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:48:33,308] [INFO] Task succeeded: Prodigal
[2023-06-08 05:48:33,309] [INFO] Task started: HMMsearch
[2023-06-08 05:48:33,309] [INFO] Running command: hmmsearch --tblout GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference/reference_markers.hmm GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:48:33,531] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:48:33,532] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga8b89b7c-3e17-4ad6-a7ba-4be5caa92040/GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 05:48:33,558] [INFO] Query marker FASTA was written to GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:48:33,558] [INFO] Task started: Blastn
[2023-06-08 05:48:33,559] [INFO] Running command: blastn -query GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference/reference_markers.fasta -out GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:48:34,136] [INFO] Task succeeded: Blastn
[2023-06-08 05:48:34,139] [INFO] Selected 15 target genomes.
[2023-06-08 05:48:34,140] [INFO] Target genome list was writen to GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:48:34,144] [INFO] Task started: fastANI
[2023-06-08 05:48:34,144] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b89b7c-3e17-4ad6-a7ba-4be5caa92040/GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:48:42,397] [INFO] Task succeeded: fastANI
[2023-06-08 05:48:42,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:48:42,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:48:42,409] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 05:48:42,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 05:48:42,410] [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 hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	95.8031	423	509	95	conclusive
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	82.2037	292	509	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	82.1647	293	509	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	82.1577	288	509	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.4359	50	509	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.8264	78	509	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:48:42,413] [INFO] DFAST Taxonomy check result was written to GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:48:42,413] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:48:42,413] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:48:42,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference/checkm_data
[2023-06-08 05:48:42,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:48:42,443] [INFO] Task started: CheckM
[2023-06-08 05:48:42,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:49:15,014] [INFO] Task succeeded: CheckM
[2023-06-08 05:49:15,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:49:15,035] [INFO] ===== Completeness check finished =====
[2023-06-08 05:49:15,035] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:49:15,036] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:49:15,036] [INFO] Task started: Blastn
[2023-06-08 05:49:15,036] [INFO] Running command: blastn -query GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64b0679-7229-4579-937b-b5684f92a16d/dqc_reference/reference_markers_gtdb.fasta -out GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:49:15,810] [INFO] Task succeeded: Blastn
[2023-06-08 05:49:15,814] [INFO] Selected 12 target genomes.
[2023-06-08 05:49:15,814] [INFO] Target genome list was writen to GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:49:15,846] [INFO] Task started: fastANI
[2023-06-08 05:49:15,847] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b89b7c-3e17-4ad6-a7ba-4be5caa92040/GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:49:23,175] [INFO] Task succeeded: fastANI
[2023-06-08 05:49:23,192] [INFO] Found 12 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-08 05:49:23,193] [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_004535825.1	s__Prevotella hominis	95.8031	423	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	inconclusive
GCA_900554835.1	s__Prevotella sp900554835	95.3792	417	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_900544825.1	s__Prevotella sp900544825	82.3438	276	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCF_000157935.1	s__Prevotella copri	82.176	287	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_015074785.1	s__Prevotella sp015074785	81.945	288	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_019127135.1	s__Prevotella sp900551275	81.8658	297	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_019249655.1	s__Prevotella sp900767615	81.737	300	509	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	81.721	278	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_000436035.1	s__Prevotella sp000436035	81.3286	266	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCA_900555035.1	s__Prevotella sp900555035	81.195	240	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440225.1	s__Prevotella sp002440225	80.0062	204	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.88	98.88	0.81	0.81	2	-
GCA_900765465.1	s__Prevotella sp900765465	79.491	176	509	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:49:23,196] [INFO] GTDB search result was written to GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:49:23,196] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:49:23,200] [INFO] DFAST_QC result json was written to GCA_945487245.1_SRR7188234_bin.49_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:49:23,200] [INFO] DFAST_QC completed!
[2023-06-08 05:49:23,200] [INFO] Total running time: 0h1m2s