[2023-06-29 06:34:37,225] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:34:37,227] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:34:37,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference
[2023-06-29 06:34:40,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:34:40,809] [INFO] Task started: Prodigal
[2023-06-29 06:34:40,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg77f8f525-5021-4a0d-b3e7-86a4a04489be/GCA_020216565.1_ASM2021656v1_genomic.fna.gz | prodigal -d GCA_020216565.1_ASM2021656v1_genomic.fna/cds.fna -a GCA_020216565.1_ASM2021656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:34:47,598] [INFO] Task succeeded: Prodigal
[2023-06-29 06:34:47,599] [INFO] Task started: HMMsearch
[2023-06-29 06:34:47,599] [INFO] Running command: hmmsearch --tblout GCA_020216565.1_ASM2021656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference/reference_markers.hmm GCA_020216565.1_ASM2021656v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:34:47,879] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:34:47,880] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg77f8f525-5021-4a0d-b3e7-86a4a04489be/GCA_020216565.1_ASM2021656v1_genomic.fna.gz]
[2023-06-29 06:34:47,910] [INFO] Query marker FASTA was written to GCA_020216565.1_ASM2021656v1_genomic.fna/markers.fasta
[2023-06-29 06:34:47,910] [INFO] Task started: Blastn
[2023-06-29 06:34:47,911] [INFO] Running command: blastn -query GCA_020216565.1_ASM2021656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference/reference_markers.fasta -out GCA_020216565.1_ASM2021656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:34:48,524] [INFO] Task succeeded: Blastn
[2023-06-29 06:34:48,528] [INFO] Selected 10 target genomes.
[2023-06-29 06:34:48,528] [INFO] Target genome list was writen to GCA_020216565.1_ASM2021656v1_genomic.fna/target_genomes.txt
[2023-06-29 06:34:48,530] [INFO] Task started: fastANI
[2023-06-29 06:34:48,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f8f525-5021-4a0d-b3e7-86a4a04489be/GCA_020216565.1_ASM2021656v1_genomic.fna.gz --refList GCA_020216565.1_ASM2021656v1_genomic.fna/target_genomes.txt --output GCA_020216565.1_ASM2021656v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:34:56,186] [INFO] Task succeeded: fastANI
[2023-06-29 06:34:56,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:34:56,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:34:56,188] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:34:56,188] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 06:34:56,188] [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 06:34:56,191] [INFO] DFAST Taxonomy check result was written to GCA_020216565.1_ASM2021656v1_genomic.fna/tc_result.tsv
[2023-06-29 06:34:56,191] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:34:56,191] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:34:56,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference/checkm_data
[2023-06-29 06:34:56,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:34:56,229] [INFO] Task started: CheckM
[2023-06-29 06:34:56,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020216565.1_ASM2021656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020216565.1_ASM2021656v1_genomic.fna/checkm_input GCA_020216565.1_ASM2021656v1_genomic.fna/checkm_result
[2023-06-29 06:35:22,930] [INFO] Task succeeded: CheckM
[2023-06-29 06:35:22,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:35:22,956] [INFO] ===== Completeness check finished =====
[2023-06-29 06:35:22,956] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:35:22,957] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020216565.1_ASM2021656v1_genomic.fna/markers.fasta)
[2023-06-29 06:35:22,957] [INFO] Task started: Blastn
[2023-06-29 06:35:22,958] [INFO] Running command: blastn -query GCA_020216565.1_ASM2021656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c5e1531-c56a-41e3-8484-eb97f235e624/dqc_reference/reference_markers_gtdb.fasta -out GCA_020216565.1_ASM2021656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:35:23,723] [INFO] Task succeeded: Blastn
[2023-06-29 06:35:23,727] [INFO] Selected 16 target genomes.
[2023-06-29 06:35:23,727] [INFO] Target genome list was writen to GCA_020216565.1_ASM2021656v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:35:23,737] [INFO] Task started: fastANI
[2023-06-29 06:35:23,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg77f8f525-5021-4a0d-b3e7-86a4a04489be/GCA_020216565.1_ASM2021656v1_genomic.fna.gz --refList GCA_020216565.1_ASM2021656v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020216565.1_ASM2021656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:35:34,546] [INFO] Task succeeded: fastANI
[2023-06-29 06:35:34,565] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:35:34,565] [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_903837815.1	s__OLB14 sp903837815	80.4693	365	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234555.1	s__OLB14 sp016234555	80.2775	427	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599285.1	s__OLB14 sp003599285	77.5481	142	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696595.1	s__OLB14 sp900696595	77.2642	178	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.68	97.00	0.88	0.84	4	-
GCA_016234495.1	s__OLB14 sp016234495	77.244	158	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235445.1	s__OLB14 sp016235445	77.0538	167	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017985935.1	s__OLB14 sp017985935	76.9593	138	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	99.53	99.53	0.94	0.94	2	-
GCA_002473085.1	s__UBA7227 sp002473085	76.9003	119	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA7227	95.0	98.42	98.07	0.85	0.72	10	-
GCA_016191845.1	s__JACPVF01 sp016191845	76.8077	137	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JACPVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360875.1	s__UBA12294 sp013360875	76.6709	129	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234535.1	s__OLB14 sp016234535	76.6294	125	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885525.1	s__OLB14 sp009885525	76.6039	114	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235425.1	s__OLB14 sp016235425	76.5418	115	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219545.1	s__OLB14 sp016219545	76.4442	108	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418205.1	s__UBA12294 sp002418205	76.1777	89	702	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.83	99.80	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-29 06:35:34,568] [INFO] GTDB search result was written to GCA_020216565.1_ASM2021656v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:35:34,568] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:35:34,571] [INFO] DFAST_QC result json was written to GCA_020216565.1_ASM2021656v1_genomic.fna/dqc_result.json
[2023-06-29 06:35:34,571] [INFO] DFAST_QC completed!
[2023-06-29 06:35:34,571] [INFO] Total running time: 0h0m57s