[2023-06-18 18:10:12,841] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:12,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:12,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference
[2023-06-18 18:10:15,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:15,138] [INFO] Task started: Prodigal
[2023-06-18 18:10:15,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg318eb95a-8e8d-472d-9b63-a67932056866/GCA_018264835.1_ASM1826483v1_genomic.fna.gz | prodigal -d GCA_018264835.1_ASM1826483v1_genomic.fna/cds.fna -a GCA_018264835.1_ASM1826483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:17,838] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:17,839] [INFO] Task started: HMMsearch
[2023-06-18 18:10:17,839] [INFO] Running command: hmmsearch --tblout GCA_018264835.1_ASM1826483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference/reference_markers.hmm GCA_018264835.1_ASM1826483v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:18,052] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:18,053] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg318eb95a-8e8d-472d-9b63-a67932056866/GCA_018264835.1_ASM1826483v1_genomic.fna.gz]
[2023-06-18 18:10:18,082] [INFO] Query marker FASTA was written to GCA_018264835.1_ASM1826483v1_genomic.fna/markers.fasta
[2023-06-18 18:10:18,082] [INFO] Task started: Blastn
[2023-06-18 18:10:18,082] [INFO] Running command: blastn -query GCA_018264835.1_ASM1826483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference/reference_markers.fasta -out GCA_018264835.1_ASM1826483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:19,330] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:19,336] [INFO] Selected 21 target genomes.
[2023-06-18 18:10:19,336] [INFO] Target genome list was writen to GCA_018264835.1_ASM1826483v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:19,343] [INFO] Task started: fastANI
[2023-06-18 18:10:19,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg318eb95a-8e8d-472d-9b63-a67932056866/GCA_018264835.1_ASM1826483v1_genomic.fna.gz --refList GCA_018264835.1_ASM1826483v1_genomic.fna/target_genomes.txt --output GCA_018264835.1_ASM1826483v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:27,620] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:27,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:27,622] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:27,624] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:27,624] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:10:27,624] [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
--------------------------------------------------------------------------------
[2023-06-18 18:10:27,648] [INFO] DFAST Taxonomy check result was written to GCA_018264835.1_ASM1826483v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:27,648] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:27,648] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:27,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference/checkm_data
[2023-06-18 18:10:27,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:27,674] [INFO] Task started: CheckM
[2023-06-18 18:10:27,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018264835.1_ASM1826483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018264835.1_ASM1826483v1_genomic.fna/checkm_input GCA_018264835.1_ASM1826483v1_genomic.fna/checkm_result
[2023-06-18 18:10:44,237] [INFO] Task succeeded: CheckM
[2023-06-18 18:10:44,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 1.77%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 18:10:44,260] [INFO] ===== Completeness check finished =====
[2023-06-18 18:10:44,260] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:10:44,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018264835.1_ASM1826483v1_genomic.fna/markers.fasta)
[2023-06-18 18:10:44,261] [INFO] Task started: Blastn
[2023-06-18 18:10:44,261] [INFO] Running command: blastn -query GCA_018264835.1_ASM1826483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50eb8295-b934-4ca1-960c-9fc75c142aa7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018264835.1_ASM1826483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:45,038] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:45,060] [INFO] Selected 17 target genomes.
[2023-06-18 18:10:45,061] [INFO] Target genome list was writen to GCA_018264835.1_ASM1826483v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:10:45,079] [INFO] Task started: fastANI
[2023-06-18 18:10:45,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg318eb95a-8e8d-472d-9b63-a67932056866/GCA_018264835.1_ASM1826483v1_genomic.fna.gz --refList GCA_018264835.1_ASM1826483v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018264835.1_ASM1826483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:10:49,941] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:49,957] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:10:49,958] [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_003534295.1	s__CAG-273 sp003534295	99.0431	376	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.76	98.52	0.84	0.83	5	conclusive
GCA_003507395.1	s__CAG-273 sp003507395	83.3223	299	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	99.04	98.89	0.89	0.87	5	-
GCA_900553865.1	s__UMGS1663 sp900553865	78.5968	137	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	98.42	98.10	0.81	0.79	3	-
GCA_017937285.1	s__CAG-492 sp017937285	78.3235	130	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525075.1	s__CAG-269 sp003525075	78.0854	129	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.02	98.89	0.90	0.88	5	-
GCA_900553405.1	s__UMGS1663 sp900553405	78.0282	146	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198755.1	s__HGM13634 sp905198755	78.0156	102	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438355.1	s__CAG-273 sp000438355	77.7855	127	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	98.50	98.37	0.86	0.79	3	-
GCA_905215935.1	s__CAG-492 sp905215935	77.6748	143	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770385.1	s__HGM13634 sp900770385	77.5273	116	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__HGM13634	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555835.1	s__UMGS1864 sp900555835	77.517	107	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1864	95.0	99.90	99.90	0.84	0.84	2	-
GCA_000434015.1	s__CAG-492 sp000434015	77.5102	161	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.68	99.35	0.94	0.91	3	-
GCA_000437215.1	s__CAG-269 sp000437215	77.4104	129	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
GCA_904420285.1	s__CAG-273 sp904420285	77.1366	127	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-273	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437145.1	s__CAG-452 sp017437145	76.7991	104	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-452	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900762425.1	s__CAG-269 sp900762425	76.7675	123	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512025.1	s__CAG-492 sp017512025	76.3572	76	493	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:10:49,960] [INFO] GTDB search result was written to GCA_018264835.1_ASM1826483v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:10:49,960] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:10:49,966] [INFO] DFAST_QC result json was written to GCA_018264835.1_ASM1826483v1_genomic.fna/dqc_result.json
[2023-06-18 18:10:49,967] [INFO] DFAST_QC completed!
[2023-06-18 18:10:49,967] [INFO] Total running time: 0h0m37s