[2023-06-29 00:37:18,357] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:37:18,387] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:37:18,387] [INFO] DQC Reference Directory: /var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference
[2023-06-29 00:37:19,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:37:19,684] [INFO] Task started: Prodigal
[2023-06-29 00:37:19,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg56d4fb87-fb43-494c-9ed9-f18369e065d7/GCA_017556405.1_ASM1755640v1_genomic.fna.gz | prodigal -d GCA_017556405.1_ASM1755640v1_genomic.fna/cds.fna -a GCA_017556405.1_ASM1755640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:37:24,882] [INFO] Task succeeded: Prodigal
[2023-06-29 00:37:24,883] [INFO] Task started: HMMsearch
[2023-06-29 00:37:24,883] [INFO] Running command: hmmsearch --tblout GCA_017556405.1_ASM1755640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference/reference_markers.hmm GCA_017556405.1_ASM1755640v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:37:25,123] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:37:25,125] [INFO] Found 6/6 markers.
[2023-06-29 00:37:25,152] [INFO] Query marker FASTA was written to GCA_017556405.1_ASM1755640v1_genomic.fna/markers.fasta
[2023-06-29 00:37:25,152] [INFO] Task started: Blastn
[2023-06-29 00:37:25,152] [INFO] Running command: blastn -query GCA_017556405.1_ASM1755640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference/reference_markers.fasta -out GCA_017556405.1_ASM1755640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:37:25,819] [INFO] Task succeeded: Blastn
[2023-06-29 00:37:25,823] [INFO] Selected 31 target genomes.
[2023-06-29 00:37:25,823] [INFO] Target genome list was writen to GCA_017556405.1_ASM1755640v1_genomic.fna/target_genomes.txt
[2023-06-29 00:37:25,828] [INFO] Task started: fastANI
[2023-06-29 00:37:25,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg56d4fb87-fb43-494c-9ed9-f18369e065d7/GCA_017556405.1_ASM1755640v1_genomic.fna.gz --refList GCA_017556405.1_ASM1755640v1_genomic.fna/target_genomes.txt --output GCA_017556405.1_ASM1755640v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:37:45,526] [INFO] Task succeeded: fastANI
[2023-06-29 00:37:45,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:37:45,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:37:45,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:37:45,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 00:37:45,530] [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
--------------------------------------------------------------------------------
[2023-06-29 00:37:45,555] [INFO] DFAST Taxonomy check result was written to GCA_017556405.1_ASM1755640v1_genomic.fna/tc_result.tsv
[2023-06-29 00:37:45,556] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:37:45,556] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:37:45,556] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference/checkm_data
[2023-06-29 00:37:45,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:37:45,591] [INFO] Task started: CheckM
[2023-06-29 00:37:45,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017556405.1_ASM1755640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017556405.1_ASM1755640v1_genomic.fna/checkm_input GCA_017556405.1_ASM1755640v1_genomic.fna/checkm_result
[2023-06-29 00:38:09,547] [INFO] Task succeeded: CheckM
[2023-06-29 00:38:09,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.97%
Contamintation: 8.33%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-29 00:38:09,576] [INFO] ===== Completeness check finished =====
[2023-06-29 00:38:09,577] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:38:09,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017556405.1_ASM1755640v1_genomic.fna/markers.fasta)
[2023-06-29 00:38:09,578] [INFO] Task started: Blastn
[2023-06-29 00:38:09,578] [INFO] Running command: blastn -query GCA_017556405.1_ASM1755640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51ade164-abce-46d8-a566-02d9de4271a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_017556405.1_ASM1755640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:10,499] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:10,503] [INFO] Selected 14 target genomes.
[2023-06-29 00:38:10,503] [INFO] Target genome list was writen to GCA_017556405.1_ASM1755640v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:38:10,509] [INFO] Task started: fastANI
[2023-06-29 00:38:10,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg56d4fb87-fb43-494c-9ed9-f18369e065d7/GCA_017556405.1_ASM1755640v1_genomic.fna.gz --refList GCA_017556405.1_ASM1755640v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017556405.1_ASM1755640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:38:17,471] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:17,481] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:38:17,481] [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_017553505.1	s__UBA1258 sp017553505	99.1266	537	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1258	95.0	96.52	96.39	0.88	0.84	3	conclusive
GCA_900100895.1	s__UBA1258 sp900100895	94.6736	514	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017544835.1	s__UBA1258 sp017544835	86.9702	457	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291405.1	s__UBA1258 sp016291405	78.4189	126	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1258	95.0	95.94	95.94	0.88	0.88	2	-
GCA_002308235.1	s__UBA1258 sp002308235	78.2266	84	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1258	95.0	96.55	96.55	0.86	0.86	2	-
GCA_016283575.1	s__UBA1258 sp016283575	77.6473	66	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1258	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619295.1	s__G11 sp017619295	77.5045	60	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900103495.1	s__G11 sp900103495	77.1642	66	564	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__G11	95.0	95.96	95.52	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 00:38:17,483] [INFO] GTDB search result was written to GCA_017556405.1_ASM1755640v1_genomic.fna/result_gtdb.tsv
[2023-06-29 00:38:17,484] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:38:17,487] [INFO] DFAST_QC result json was written to GCA_017556405.1_ASM1755640v1_genomic.fna/dqc_result.json
[2023-06-29 00:38:17,488] [INFO] DFAST_QC completed!
[2023-06-29 00:38:17,488] [INFO] Total running time: 0h0m59s