[2023-06-29 22:44:14,206] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:44:14,210] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:44:14,210] [INFO] DQC Reference Directory: /var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference
[2023-06-29 22:44:15,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:44:15,513] [INFO] Task started: Prodigal
[2023-06-29 22:44:15,513] [INFO] Running command: gunzip -c /var/lib/cwl/stga27fd2d5-67ef-4184-bb61-619da95fd983/GCA_016290905.1_ASM1629090v1_genomic.fna.gz | prodigal -d GCA_016290905.1_ASM1629090v1_genomic.fna/cds.fna -a GCA_016290905.1_ASM1629090v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:44:21,476] [INFO] Task succeeded: Prodigal
[2023-06-29 22:44:21,477] [INFO] Task started: HMMsearch
[2023-06-29 22:44:21,477] [INFO] Running command: hmmsearch --tblout GCA_016290905.1_ASM1629090v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference/reference_markers.hmm GCA_016290905.1_ASM1629090v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:44:21,722] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:44:21,724] [INFO] Found 6/6 markers.
[2023-06-29 22:44:21,751] [INFO] Query marker FASTA was written to GCA_016290905.1_ASM1629090v1_genomic.fna/markers.fasta
[2023-06-29 22:44:21,751] [INFO] Task started: Blastn
[2023-06-29 22:44:21,751] [INFO] Running command: blastn -query GCA_016290905.1_ASM1629090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference/reference_markers.fasta -out GCA_016290905.1_ASM1629090v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:44:22,333] [INFO] Task succeeded: Blastn
[2023-06-29 22:44:22,337] [INFO] Selected 23 target genomes.
[2023-06-29 22:44:22,337] [INFO] Target genome list was writen to GCA_016290905.1_ASM1629090v1_genomic.fna/target_genomes.txt
[2023-06-29 22:44:22,342] [INFO] Task started: fastANI
[2023-06-29 22:44:22,342] [INFO] Running command: fastANI --query /var/lib/cwl/stga27fd2d5-67ef-4184-bb61-619da95fd983/GCA_016290905.1_ASM1629090v1_genomic.fna.gz --refList GCA_016290905.1_ASM1629090v1_genomic.fna/target_genomes.txt --output GCA_016290905.1_ASM1629090v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:44:33,349] [INFO] Task succeeded: fastANI
[2023-06-29 22:44:33,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:44:33,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:44:33,351] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:44:33,352] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 22:44:33,352] [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 22:44:33,354] [INFO] DFAST Taxonomy check result was written to GCA_016290905.1_ASM1629090v1_genomic.fna/tc_result.tsv
[2023-06-29 22:44:33,354] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:44:33,354] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:44:33,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference/checkm_data
[2023-06-29 22:44:33,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:44:33,391] [INFO] Task started: CheckM
[2023-06-29 22:44:33,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016290905.1_ASM1629090v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016290905.1_ASM1629090v1_genomic.fna/checkm_input GCA_016290905.1_ASM1629090v1_genomic.fna/checkm_result
[2023-06-29 22:44:57,957] [INFO] Task succeeded: CheckM
[2023-06-29 22:44:57,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.22%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 22:44:57,981] [INFO] ===== Completeness check finished =====
[2023-06-29 22:44:57,981] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:44:57,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016290905.1_ASM1629090v1_genomic.fna/markers.fasta)
[2023-06-29 22:44:57,982] [INFO] Task started: Blastn
[2023-06-29 22:44:57,982] [INFO] Running command: blastn -query GCA_016290905.1_ASM1629090v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7298105e-9d87-4d8b-8e68-e2dd68b6463a/dqc_reference/reference_markers_gtdb.fasta -out GCA_016290905.1_ASM1629090v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:44:58,777] [INFO] Task succeeded: Blastn
[2023-06-29 22:44:58,782] [INFO] Selected 15 target genomes.
[2023-06-29 22:44:58,783] [INFO] Target genome list was writen to GCA_016290905.1_ASM1629090v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:44:58,791] [INFO] Task started: fastANI
[2023-06-29 22:44:58,791] [INFO] Running command: fastANI --query /var/lib/cwl/stga27fd2d5-67ef-4184-bb61-619da95fd983/GCA_016290905.1_ASM1629090v1_genomic.fna.gz --refList GCA_016290905.1_ASM1629090v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016290905.1_ASM1629090v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:45:06,222] [INFO] Task succeeded: fastANI
[2023-06-29 22:45:06,240] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:45:06,240] [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_016290905.1	s__RUG11977 sp016290905	100.0	870	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017427415.1	s__RUG11977 sp017427415	79.7164	241	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	97.56	97.25	0.92	0.88	5	-
GCA_016285135.1	s__RUG11977 sp016285135	79.5029	55	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	98.61	98.52	0.82	0.80	3	-
GCA_017542245.1	s__RUG11977 sp017542245	79.2443	249	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774525.1	s__RUG11977 sp902774525	78.9693	185	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	97.96	97.96	0.96	0.96	2	-
GCA_017620375.1	s__RUG11977 sp017620375	78.8966	201	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	96.82	96.22	0.78	0.75	4	-
GCA_016287095.1	s__RUG11977 sp016287095	78.7649	207	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	98.70	98.70	0.84	0.84	2	-
GCA_016288005.1	s__RUG11977 sp016288005	78.592	69	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	96.56	96.56	0.91	0.91	2	-
GCA_017553965.1	s__RUG11977 sp017553965	78.495	114	881	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG11977	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:45:06,243] [INFO] GTDB search result was written to GCA_016290905.1_ASM1629090v1_genomic.fna/result_gtdb.tsv
[2023-06-29 22:45:06,244] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:45:06,247] [INFO] DFAST_QC result json was written to GCA_016290905.1_ASM1629090v1_genomic.fna/dqc_result.json
[2023-06-29 22:45:06,247] [INFO] DFAST_QC completed!
[2023-06-29 22:45:06,247] [INFO] Total running time: 0h0m52s