[2023-06-17 12:24:50,694] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:50,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:50,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference
[2023-06-17 12:24:52,333] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:52,334] [INFO] Task started: Prodigal
[2023-06-17 12:24:52,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f3496f2-c975-4c1f-88ed-3d3af0282208/GCA_028705735.1_ASM2870573v1_genomic.fna.gz | prodigal -d GCA_028705735.1_ASM2870573v1_genomic.fna/cds.fna -a GCA_028705735.1_ASM2870573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:25:07,377] [INFO] Task succeeded: Prodigal
[2023-06-17 12:25:07,377] [INFO] Task started: HMMsearch
[2023-06-17 12:25:07,378] [INFO] Running command: hmmsearch --tblout GCA_028705735.1_ASM2870573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference/reference_markers.hmm GCA_028705735.1_ASM2870573v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:25:07,706] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:25:07,708] [INFO] Found 6/6 markers.
[2023-06-17 12:25:07,738] [INFO] Query marker FASTA was written to GCA_028705735.1_ASM2870573v1_genomic.fna/markers.fasta
[2023-06-17 12:25:07,738] [INFO] Task started: Blastn
[2023-06-17 12:25:07,738] [INFO] Running command: blastn -query GCA_028705735.1_ASM2870573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference/reference_markers.fasta -out GCA_028705735.1_ASM2870573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:25:08,334] [INFO] Task succeeded: Blastn
[2023-06-17 12:25:08,338] [INFO] Selected 31 target genomes.
[2023-06-17 12:25:08,339] [INFO] Target genome list was writen to GCA_028705735.1_ASM2870573v1_genomic.fna/target_genomes.txt
[2023-06-17 12:25:08,343] [INFO] Task started: fastANI
[2023-06-17 12:25:08,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f3496f2-c975-4c1f-88ed-3d3af0282208/GCA_028705735.1_ASM2870573v1_genomic.fna.gz --refList GCA_028705735.1_ASM2870573v1_genomic.fna/target_genomes.txt --output GCA_028705735.1_ASM2870573v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:25:27,589] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:27,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:25:27,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:25:27,593] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:25:27,593] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 12:25:27,593] [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
--------------------------------------------------------------------------------
[2023-06-17 12:25:27,596] [INFO] DFAST Taxonomy check result was written to GCA_028705735.1_ASM2870573v1_genomic.fna/tc_result.tsv
[2023-06-17 12:25:27,600] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:25:27,601] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:25:27,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference/checkm_data
[2023-06-17 12:25:27,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:25:27,643] [INFO] Task started: CheckM
[2023-06-17 12:25:27,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028705735.1_ASM2870573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028705735.1_ASM2870573v1_genomic.fna/checkm_input GCA_028705735.1_ASM2870573v1_genomic.fna/checkm_result
[2023-06-17 12:26:12,873] [INFO] Task succeeded: CheckM
[2023-06-17 12:26:12,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 8.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 12:26:12,921] [INFO] ===== Completeness check finished =====
[2023-06-17 12:26:12,921] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:26:12,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028705735.1_ASM2870573v1_genomic.fna/markers.fasta)
[2023-06-17 12:26:12,922] [INFO] Task started: Blastn
[2023-06-17 12:26:12,922] [INFO] Running command: blastn -query GCA_028705735.1_ASM2870573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg462b74c9-5b2b-4acb-ab05-4f85c3f448d7/dqc_reference/reference_markers_gtdb.fasta -out GCA_028705735.1_ASM2870573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:26:13,719] [INFO] Task succeeded: Blastn
[2023-06-17 12:26:13,724] [INFO] Selected 16 target genomes.
[2023-06-17 12:26:13,724] [INFO] Target genome list was writen to GCA_028705735.1_ASM2870573v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:26:13,728] [INFO] Task started: fastANI
[2023-06-17 12:26:13,728] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f3496f2-c975-4c1f-88ed-3d3af0282208/GCA_028705735.1_ASM2870573v1_genomic.fna.gz --refList GCA_028705735.1_ASM2870573v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028705735.1_ASM2870573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:26:20,349] [INFO] Task succeeded: fastANI
[2023-06-17 12:26:20,363] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:26:20,363] [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_012515395.1	s__DMER64 sp012515395	98.7691	371	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	96.65	96.56	0.76	0.55	3	conclusive
GCA_011620605.1	s__DMER64 sp011620605	84.5322	527	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002408205.1	s__DMER64 sp002408205	82.3022	193	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	98.33	97.78	0.90	0.86	4	-
GCA_001512865.1	s__DMER64 sp001512865	80.9217	290	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.73	99.73	0.89	0.89	2	-
GCA_002070565.1	s__DMER64 sp002070565	78.8945	212	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.14	99.14	0.85	0.85	2	-
GCA_001603455.1	s__DMER64 sp001603455	78.4166	233	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.83	99.68	0.89	0.76	4	-
GCA_002409325.1	s__DMER64 sp002409325	78.1245	247	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305545.1	s__DMER64 sp002305545	78.0825	236	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	99.79	99.75	0.96	0.96	3	-
GCA_002071175.1	s__DMER64 sp002071175	77.9311	166	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839605.1	s__DMER64 sp012839605	76.9376	83	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012510445.1	s__DMER64 sp012510445	76.6636	100	811	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__DMER64	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:26:20,365] [INFO] GTDB search result was written to GCA_028705735.1_ASM2870573v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:26:20,366] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:26:20,368] [INFO] DFAST_QC result json was written to GCA_028705735.1_ASM2870573v1_genomic.fna/dqc_result.json
[2023-06-17 12:26:20,369] [INFO] DFAST_QC completed!
[2023-06-17 12:26:20,369] [INFO] Total running time: 0h1m30s