[2023-06-04 18:26:19,161] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:26:19,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:26:19,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference
[2023-06-04 18:26:20,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:26:20,535] [INFO] Task started: Prodigal
[2023-06-04 18:26:20,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg82c43004-f626-4ceb-8a89-9ef0a04affef/GCA_004556975.1_ASM455697v1_genomic.fna.gz | prodigal -d GCA_004556975.1_ASM455697v1_genomic.fna/cds.fna -a GCA_004556975.1_ASM455697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:26:24,669] [INFO] Task succeeded: Prodigal
[2023-06-04 18:26:24,669] [INFO] Task started: HMMsearch
[2023-06-04 18:26:24,669] [INFO] Running command: hmmsearch --tblout GCA_004556975.1_ASM455697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference/reference_markers.hmm GCA_004556975.1_ASM455697v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:26:24,911] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:26:24,913] [INFO] Found 6/6 markers.
[2023-06-04 18:26:24,944] [INFO] Query marker FASTA was written to GCA_004556975.1_ASM455697v1_genomic.fna/markers.fasta
[2023-06-04 18:26:24,945] [INFO] Task started: Blastn
[2023-06-04 18:26:24,945] [INFO] Running command: blastn -query GCA_004556975.1_ASM455697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference/reference_markers.fasta -out GCA_004556975.1_ASM455697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:25,648] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:25,653] [INFO] Selected 23 target genomes.
[2023-06-04 18:26:25,653] [INFO] Target genome list was writen to GCA_004556975.1_ASM455697v1_genomic.fna/target_genomes.txt
[2023-06-04 18:26:25,847] [INFO] Task started: fastANI
[2023-06-04 18:26:25,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg82c43004-f626-4ceb-8a89-9ef0a04affef/GCA_004556975.1_ASM455697v1_genomic.fna.gz --refList GCA_004556975.1_ASM455697v1_genomic.fna/target_genomes.txt --output GCA_004556975.1_ASM455697v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:26:38,047] [INFO] Task succeeded: fastANI
[2023-06-04 18:26:38,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:26:38,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:26:38,050] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:26:38,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 18:26:38,051] [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
--------------------------------------------------------------------------------
[2023-06-04 18:26:38,053] [INFO] DFAST Taxonomy check result was written to GCA_004556975.1_ASM455697v1_genomic.fna/tc_result.tsv
[2023-06-04 18:26:38,054] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:26:38,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:26:38,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference/checkm_data
[2023-06-04 18:26:38,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:26:38,082] [INFO] Task started: CheckM
[2023-06-04 18:26:38,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004556975.1_ASM455697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004556975.1_ASM455697v1_genomic.fna/checkm_input GCA_004556975.1_ASM455697v1_genomic.fna/checkm_result
[2023-06-04 18:26:57,382] [INFO] Task succeeded: CheckM
[2023-06-04 18:26:57,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:26:57,403] [INFO] ===== Completeness check finished =====
[2023-06-04 18:26:57,404] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:26:57,404] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004556975.1_ASM455697v1_genomic.fna/markers.fasta)
[2023-06-04 18:26:57,405] [INFO] Task started: Blastn
[2023-06-04 18:26:57,405] [INFO] Running command: blastn -query GCA_004556975.1_ASM455697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24b6f81b-4f44-45fc-9a91-99699705c77e/dqc_reference/reference_markers_gtdb.fasta -out GCA_004556975.1_ASM455697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:58,487] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:58,493] [INFO] Selected 15 target genomes.
[2023-06-04 18:26:58,494] [INFO] Target genome list was writen to GCA_004556975.1_ASM455697v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:26:58,774] [INFO] Task started: fastANI
[2023-06-04 18:26:58,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg82c43004-f626-4ceb-8a89-9ef0a04affef/GCA_004556975.1_ASM455697v1_genomic.fna.gz --refList GCA_004556975.1_ASM455697v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004556975.1_ASM455697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:27:04,012] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:04,025] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:27:04,026] [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_004556975.1	s__UMGS1668 sp004556975	100.0	504	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	97.44	96.73	0.87	0.85	6	conclusive
GCA_900553955.1	s__UMGS1668 sp900553955	84.8464	331	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	98.96	97.93	0.95	0.91	3	-
GCA_900768105.1	s__UMGS1668 sp900768105	83.1943	362	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018110905.1	s__UMGS1668 sp018110905	78.7158	153	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	97.78	97.78	0.91	0.91	2	-
GCA_017473745.1	s__UMGS1668 sp017473745	78.3626	167	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296485.1	s__UMGS1668 sp016296485	78.3089	133	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017547705.1	s__UMGS1668 sp017547705	77.893	127	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435745.1	s__UMGS1668 sp017435745	77.7017	122	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067315.1	s__UMGS1668 sp015067315	77.6427	151	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017399765.1	s__UMGS1668 sp017399765	77.6196	153	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436125.1	s__UMGS1668 sp017436125	77.4353	136	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067125.1	s__UMGS1668 sp015067125	77.4098	128	508	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UMGS1668	95.0	97.47	97.35	0.81	0.76	4	-
--------------------------------------------------------------------------------
[2023-06-04 18:27:04,028] [INFO] GTDB search result was written to GCA_004556975.1_ASM455697v1_genomic.fna/result_gtdb.tsv
[2023-06-04 18:27:04,029] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:27:04,032] [INFO] DFAST_QC result json was written to GCA_004556975.1_ASM455697v1_genomic.fna/dqc_result.json
[2023-06-04 18:27:04,033] [INFO] DFAST_QC completed!
[2023-06-04 18:27:04,033] [INFO] Total running time: 0h0m45s