[2023-06-28 05:38:02,255] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:38:02,260] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:38:02,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference
[2023-06-28 05:38:03,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:38:03,853] [INFO] Task started: Prodigal
[2023-06-28 05:38:03,853] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5203642-dca8-4d61-a307-5fe3b18d094b/GCA_017455345.1_ASM1745534v1_genomic.fna.gz | prodigal -d GCA_017455345.1_ASM1745534v1_genomic.fna/cds.fna -a GCA_017455345.1_ASM1745534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:38:15,913] [INFO] Task succeeded: Prodigal
[2023-06-28 05:38:15,914] [INFO] Task started: HMMsearch
[2023-06-28 05:38:15,915] [INFO] Running command: hmmsearch --tblout GCA_017455345.1_ASM1745534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference/reference_markers.hmm GCA_017455345.1_ASM1745534v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:38:16,136] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:38:16,138] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5203642-dca8-4d61-a307-5fe3b18d094b/GCA_017455345.1_ASM1745534v1_genomic.fna.gz]
[2023-06-28 05:38:16,163] [INFO] Query marker FASTA was written to GCA_017455345.1_ASM1745534v1_genomic.fna/markers.fasta
[2023-06-28 05:38:16,163] [INFO] Task started: Blastn
[2023-06-28 05:38:16,164] [INFO] Running command: blastn -query GCA_017455345.1_ASM1745534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference/reference_markers.fasta -out GCA_017455345.1_ASM1745534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:38:19,029] [INFO] Task succeeded: Blastn
[2023-06-28 05:38:19,034] [INFO] Selected 25 target genomes.
[2023-06-28 05:38:19,035] [INFO] Target genome list was writen to GCA_017455345.1_ASM1745534v1_genomic.fna/target_genomes.txt
[2023-06-28 05:38:19,050] [INFO] Task started: fastANI
[2023-06-28 05:38:19,051] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5203642-dca8-4d61-a307-5fe3b18d094b/GCA_017455345.1_ASM1745534v1_genomic.fna.gz --refList GCA_017455345.1_ASM1745534v1_genomic.fna/target_genomes.txt --output GCA_017455345.1_ASM1745534v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:38:36,608] [INFO] Task succeeded: fastANI
[2023-06-28 05:38:36,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:38:36,609] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:38:36,611] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:38:36,611] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 05:38:36,611] [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 05:38:36,613] [INFO] DFAST Taxonomy check result was written to GCA_017455345.1_ASM1745534v1_genomic.fna/tc_result.tsv
[2023-06-28 05:38:36,614] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:38:36,614] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:38:36,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference/checkm_data
[2023-06-28 05:38:36,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:38:36,644] [INFO] Task started: CheckM
[2023-06-28 05:38:36,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017455345.1_ASM1745534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017455345.1_ASM1745534v1_genomic.fna/checkm_input GCA_017455345.1_ASM1745534v1_genomic.fna/checkm_result
[2023-06-28 05:39:13,906] [INFO] Task succeeded: CheckM
[2023-06-28 05:39:13,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.29%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:39:13,931] [INFO] ===== Completeness check finished =====
[2023-06-28 05:39:13,931] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:39:13,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017455345.1_ASM1745534v1_genomic.fna/markers.fasta)
[2023-06-28 05:39:13,932] [INFO] Task started: Blastn
[2023-06-28 05:39:13,932] [INFO] Running command: blastn -query GCA_017455345.1_ASM1745534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg208e81f6-21b5-4c79-8f46-057ec28e7db2/dqc_reference/reference_markers_gtdb.fasta -out GCA_017455345.1_ASM1745534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:39:14,718] [INFO] Task succeeded: Blastn
[2023-06-28 05:39:14,722] [INFO] Selected 11 target genomes.
[2023-06-28 05:39:14,722] [INFO] Target genome list was writen to GCA_017455345.1_ASM1745534v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:39:14,732] [INFO] Task started: fastANI
[2023-06-28 05:39:14,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5203642-dca8-4d61-a307-5fe3b18d094b/GCA_017455345.1_ASM1745534v1_genomic.fna.gz --refList GCA_017455345.1_ASM1745534v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017455345.1_ASM1745534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:39:18,702] [INFO] Task succeeded: fastANI
[2023-06-28 05:39:18,716] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 05:39:18,717] [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_902787255.1	s__Cryptobacteroides sp902787255	95.2748	295	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.77	95.77	0.63	0.63	2	conclusive
GCA_017962705.1	s__Cryptobacteroides sp017962705	85.4605	275	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784785.1	s__Cryptobacteroides sp902784785	85.3264	294	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795445.1	s__Cryptobacteroides sp902795445	79.9494	182	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961345.1	s__Cryptobacteroides sp017961345	78.7871	141	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318565.1	s__Cryptobacteroides sp900318565	76.7139	51	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.62	96.86	0.83	0.73	9	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	76.6422	56	539	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
--------------------------------------------------------------------------------
[2023-06-28 05:39:18,719] [INFO] GTDB search result was written to GCA_017455345.1_ASM1745534v1_genomic.fna/result_gtdb.tsv
[2023-06-28 05:39:18,720] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:39:18,723] [INFO] DFAST_QC result json was written to GCA_017455345.1_ASM1745534v1_genomic.fna/dqc_result.json
[2023-06-28 05:39:18,724] [INFO] DFAST_QC completed!
[2023-06-28 05:39:18,724] [INFO] Total running time: 0h1m16s