[2023-06-19 12:10:44,478] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:44,481] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:44,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference
[2023-06-19 12:10:45,764] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:45,765] [INFO] Task started: Prodigal
[2023-06-19 12:10:45,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d67da3e-c380-4f8a-bb31-5f38e41414f5/GCA_018702555.1_ASM1870255v1_genomic.fna.gz | prodigal -d GCA_018702555.1_ASM1870255v1_genomic.fna/cds.fna -a GCA_018702555.1_ASM1870255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:48,161] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:48,161] [INFO] Task started: HMMsearch
[2023-06-19 12:10:48,161] [INFO] Running command: hmmsearch --tblout GCA_018702555.1_ASM1870255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference/reference_markers.hmm GCA_018702555.1_ASM1870255v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:48,388] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:48,389] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8d67da3e-c380-4f8a-bb31-5f38e41414f5/GCA_018702555.1_ASM1870255v1_genomic.fna.gz]
[2023-06-19 12:10:48,411] [INFO] Query marker FASTA was written to GCA_018702555.1_ASM1870255v1_genomic.fna/markers.fasta
[2023-06-19 12:10:48,411] [INFO] Task started: Blastn
[2023-06-19 12:10:48,411] [INFO] Running command: blastn -query GCA_018702555.1_ASM1870255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference/reference_markers.fasta -out GCA_018702555.1_ASM1870255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:48,901] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:48,906] [INFO] Selected 5 target genomes.
[2023-06-19 12:10:48,906] [INFO] Target genome list was writen to GCA_018702555.1_ASM1870255v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:48,909] [INFO] Task started: fastANI
[2023-06-19 12:10:48,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d67da3e-c380-4f8a-bb31-5f38e41414f5/GCA_018702555.1_ASM1870255v1_genomic.fna.gz --refList GCA_018702555.1_ASM1870255v1_genomic.fna/target_genomes.txt --output GCA_018702555.1_ASM1870255v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:10:50,516] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:50,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:10:50,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:10:50,518] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:10:50,519] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:10:50,519] [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
--------------------------------------------------------------------------------
[2023-06-19 12:10:50,521] [INFO] DFAST Taxonomy check result was written to GCA_018702555.1_ASM1870255v1_genomic.fna/tc_result.tsv
[2023-06-19 12:10:50,522] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:10:50,522] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:50,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference/checkm_data
[2023-06-19 12:10:50,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:50,545] [INFO] Task started: CheckM
[2023-06-19 12:10:50,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018702555.1_ASM1870255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018702555.1_ASM1870255v1_genomic.fna/checkm_input GCA_018702555.1_ASM1870255v1_genomic.fna/checkm_result
[2023-06-19 12:11:06,191] [INFO] Task succeeded: CheckM
[2023-06-19 12:11:06,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:11:06,209] [INFO] ===== Completeness check finished =====
[2023-06-19 12:11:06,210] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:11:06,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018702555.1_ASM1870255v1_genomic.fna/markers.fasta)
[2023-06-19 12:11:06,211] [INFO] Task started: Blastn
[2023-06-19 12:11:06,211] [INFO] Running command: blastn -query GCA_018702555.1_ASM1870255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg285eae4f-4f75-4a63-a64f-616ad30aa8f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018702555.1_ASM1870255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:11:06,635] [INFO] Task succeeded: Blastn
[2023-06-19 12:11:06,639] [INFO] Selected 7 target genomes.
[2023-06-19 12:11:06,639] [INFO] Target genome list was writen to GCA_018702555.1_ASM1870255v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:11:06,643] [INFO] Task started: fastANI
[2023-06-19 12:11:06,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d67da3e-c380-4f8a-bb31-5f38e41414f5/GCA_018702555.1_ASM1870255v1_genomic.fna.gz --refList GCA_018702555.1_ASM1870255v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018702555.1_ASM1870255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:11:08,670] [INFO] Task succeeded: fastANI
[2023-06-19 12:11:08,680] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:11:08,680] [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_002494975.1	s__MGIIb-O2 sp002494975	98.5769	313	397	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.81	97.76	0.81	0.69	24	conclusive
GCA_902511005.1	s__MGIIb-O2 sp902511005	91.4106	318	397	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.72	98.72	0.78	0.78	2	-
GCA_902514485.1	s__MGIIb-O2 sp902514485	89.043	207	397	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	98.21	0.74	0.74	2	-
GCA_016777225.1	s__MGIIb-O2 sp016777225	81.1746	290	397	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002495525.1	s__MGIIb-O2 sp002495525	78.6785	167	397	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	96.68	0.79	0.75	3	-
GCA_002504905.1	s__MGIIb-O2 sp002504905	78.1601	177	397	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
--------------------------------------------------------------------------------
[2023-06-19 12:11:08,682] [INFO] GTDB search result was written to GCA_018702555.1_ASM1870255v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:11:08,683] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:11:08,685] [INFO] DFAST_QC result json was written to GCA_018702555.1_ASM1870255v1_genomic.fna/dqc_result.json
[2023-06-19 12:11:08,685] [INFO] DFAST_QC completed!
[2023-06-19 12:11:08,686] [INFO] Total running time: 0h0m24s