[2023-06-28 04:36:58,858] [INFO] DFAST_QC pipeline started.
[2023-06-28 04:36:58,860] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 04:36:58,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference
[2023-06-28 04:37:00,070] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 04:37:00,071] [INFO] Task started: Prodigal
[2023-06-28 04:37:00,071] [INFO] Running command: gunzip -c /var/lib/cwl/stgd37399eb-f9d4-41fa-b6ff-f7d9fe0059a6/GCA_017521145.1_ASM1752114v1_genomic.fna.gz | prodigal -d GCA_017521145.1_ASM1752114v1_genomic.fna/cds.fna -a GCA_017521145.1_ASM1752114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 04:37:13,103] [INFO] Task succeeded: Prodigal
[2023-06-28 04:37:13,103] [INFO] Task started: HMMsearch
[2023-06-28 04:37:13,103] [INFO] Running command: hmmsearch --tblout GCA_017521145.1_ASM1752114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference/reference_markers.hmm GCA_017521145.1_ASM1752114v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 04:37:13,330] [INFO] Task succeeded: HMMsearch
[2023-06-28 04:37:13,331] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd37399eb-f9d4-41fa-b6ff-f7d9fe0059a6/GCA_017521145.1_ASM1752114v1_genomic.fna.gz]
[2023-06-28 04:37:13,367] [INFO] Query marker FASTA was written to GCA_017521145.1_ASM1752114v1_genomic.fna/markers.fasta
[2023-06-28 04:37:13,368] [INFO] Task started: Blastn
[2023-06-28 04:37:13,368] [INFO] Running command: blastn -query GCA_017521145.1_ASM1752114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference/reference_markers.fasta -out GCA_017521145.1_ASM1752114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:37:14,077] [INFO] Task succeeded: Blastn
[2023-06-28 04:37:14,081] [INFO] Selected 22 target genomes.
[2023-06-28 04:37:14,081] [INFO] Target genome list was writen to GCA_017521145.1_ASM1752114v1_genomic.fna/target_genomes.txt
[2023-06-28 04:37:14,085] [INFO] Task started: fastANI
[2023-06-28 04:37:14,085] [INFO] Running command: fastANI --query /var/lib/cwl/stgd37399eb-f9d4-41fa-b6ff-f7d9fe0059a6/GCA_017521145.1_ASM1752114v1_genomic.fna.gz --refList GCA_017521145.1_ASM1752114v1_genomic.fna/target_genomes.txt --output GCA_017521145.1_ASM1752114v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 04:37:29,360] [INFO] Task succeeded: fastANI
[2023-06-28 04:37:29,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 04:37:29,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 04:37:29,363] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 04:37:29,363] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 04:37:29,363] [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
--------------------------------------------------------------------------------
[2023-06-28 04:37:29,365] [INFO] DFAST Taxonomy check result was written to GCA_017521145.1_ASM1752114v1_genomic.fna/tc_result.tsv
[2023-06-28 04:37:29,366] [INFO] ===== Taxonomy check completed =====
[2023-06-28 04:37:29,366] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 04:37:29,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference/checkm_data
[2023-06-28 04:37:29,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 04:37:29,393] [INFO] Task started: CheckM
[2023-06-28 04:37:29,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017521145.1_ASM1752114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017521145.1_ASM1752114v1_genomic.fna/checkm_input GCA_017521145.1_ASM1752114v1_genomic.fna/checkm_result
[2023-06-28 04:38:08,845] [INFO] Task succeeded: CheckM
[2023-06-28 04:38:08,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 04:38:08,865] [INFO] ===== Completeness check finished =====
[2023-06-28 04:38:08,865] [INFO] ===== Start GTDB Search =====
[2023-06-28 04:38:08,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017521145.1_ASM1752114v1_genomic.fna/markers.fasta)
[2023-06-28 04:38:08,866] [INFO] Task started: Blastn
[2023-06-28 04:38:08,866] [INFO] Running command: blastn -query GCA_017521145.1_ASM1752114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a0dccdf-3ac2-428e-8e99-acd2d196d9c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_017521145.1_ASM1752114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 04:38:09,851] [INFO] Task succeeded: Blastn
[2023-06-28 04:38:09,855] [INFO] Selected 9 target genomes.
[2023-06-28 04:38:09,856] [INFO] Target genome list was writen to GCA_017521145.1_ASM1752114v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 04:38:09,860] [INFO] Task started: fastANI
[2023-06-28 04:38:09,861] [INFO] Running command: fastANI --query /var/lib/cwl/stgd37399eb-f9d4-41fa-b6ff-f7d9fe0059a6/GCA_017521145.1_ASM1752114v1_genomic.fna.gz --refList GCA_017521145.1_ASM1752114v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017521145.1_ASM1752114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 04:38:14,152] [INFO] Task succeeded: fastANI
[2023-06-28 04:38:14,163] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 04:38:14,163] [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_017521145.1	s__Akkermansia sp017521145	100.0	566	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017435365.1	s__Akkermansia sp017435365	83.9926	405	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937215.1	s__Akkermansia sp017937215	83.9021	389	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	97.30	97.14	0.82	0.81	3	-
GCA_015062005.1	s__Akkermansia sp015062005	83.709	384	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017517805.1	s__Akkermansia sp017517805	83.4001	386	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904502165.1	s__Akkermansia sp904502165	83.0023	364	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017555465.1	s__Akkermansia sp017555465	82.8747	302	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501915.1	s__Akkermansia sp904501915	82.7816	364	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017504805.1	s__Akkermansia sp017504805	82.5258	319	574	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia	95.0	98.93	98.93	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-28 04:38:14,165] [INFO] GTDB search result was written to GCA_017521145.1_ASM1752114v1_genomic.fna/result_gtdb.tsv
[2023-06-28 04:38:14,165] [INFO] ===== GTDB Search completed =====
[2023-06-28 04:38:14,169] [INFO] DFAST_QC result json was written to GCA_017521145.1_ASM1752114v1_genomic.fna/dqc_result.json
[2023-06-28 04:38:14,169] [INFO] DFAST_QC completed!
[2023-06-28 04:38:14,169] [INFO] Total running time: 0h1m15s