[2023-06-28 18:27:11,149] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:27:11,151] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:27:11,152] [INFO] DQC Reference Directory: /var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference
[2023-06-28 18:27:12,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:27:12,588] [INFO] Task started: Prodigal
[2023-06-28 18:27:12,588] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ea6bfaa-7387-4249-bd91-fdf8ffc92067/GCA_015057455.1_ASM1505745v1_genomic.fna.gz | prodigal -d GCA_015057455.1_ASM1505745v1_genomic.fna/cds.fna -a GCA_015057455.1_ASM1505745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:17,336] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:17,336] [INFO] Task started: HMMsearch
[2023-06-28 18:27:17,337] [INFO] Running command: hmmsearch --tblout GCA_015057455.1_ASM1505745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference/reference_markers.hmm GCA_015057455.1_ASM1505745v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:17,598] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:17,600] [INFO] Found 6/6 markers.
[2023-06-28 18:27:17,637] [INFO] Query marker FASTA was written to GCA_015057455.1_ASM1505745v1_genomic.fna/markers.fasta
[2023-06-28 18:27:17,638] [INFO] Task started: Blastn
[2023-06-28 18:27:17,638] [INFO] Running command: blastn -query GCA_015057455.1_ASM1505745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference/reference_markers.fasta -out GCA_015057455.1_ASM1505745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:18,266] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:18,271] [INFO] Selected 24 target genomes.
[2023-06-28 18:27:18,271] [INFO] Target genome list was writen to GCA_015057455.1_ASM1505745v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:18,274] [INFO] Task started: fastANI
[2023-06-28 18:27:18,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ea6bfaa-7387-4249-bd91-fdf8ffc92067/GCA_015057455.1_ASM1505745v1_genomic.fna.gz --refList GCA_015057455.1_ASM1505745v1_genomic.fna/target_genomes.txt --output GCA_015057455.1_ASM1505745v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:34,581] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:34,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:34,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:34,588] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:34,588] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:27:34,588] [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
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	77.4985	76	917	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	76.7573	56	917	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	76.4464	61	917	95	below_threshold
Vallitalea guaymasensis	strain=Ra1766G1	GCA_018141425.1	1185412	1185412	type	True	75.8572	50	917	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:27:34,590] [INFO] DFAST Taxonomy check result was written to GCA_015057455.1_ASM1505745v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:34,591] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:34,591] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:34,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference/checkm_data
[2023-06-28 18:27:34,593] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:34,630] [INFO] Task started: CheckM
[2023-06-28 18:27:34,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015057455.1_ASM1505745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015057455.1_ASM1505745v1_genomic.fna/checkm_input GCA_015057455.1_ASM1505745v1_genomic.fna/checkm_result
[2023-06-28 18:27:56,420] [INFO] Task succeeded: CheckM
[2023-06-28 18:27:56,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:27:56,441] [INFO] ===== Completeness check finished =====
[2023-06-28 18:27:56,442] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:27:56,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015057455.1_ASM1505745v1_genomic.fna/markers.fasta)
[2023-06-28 18:27:56,443] [INFO] Task started: Blastn
[2023-06-28 18:27:56,443] [INFO] Running command: blastn -query GCA_015057455.1_ASM1505745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge47c814a-0970-444c-9754-28a5fe75696a/dqc_reference/reference_markers_gtdb.fasta -out GCA_015057455.1_ASM1505745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:57,255] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:57,260] [INFO] Selected 24 target genomes.
[2023-06-28 18:27:57,260] [INFO] Target genome list was writen to GCA_015057455.1_ASM1505745v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:27:57,278] [INFO] Task started: fastANI
[2023-06-28 18:27:57,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ea6bfaa-7387-4249-bd91-fdf8ffc92067/GCA_015057455.1_ASM1505745v1_genomic.fna.gz --refList GCA_015057455.1_ASM1505745v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015057455.1_ASM1505745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:28:09,415] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:09,430] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:28:09,430] [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_015057455.1	s__SIG301 sp015057455	100.0	912	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG301	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012070565.1	s__Anaerosporobacter sp012070565	77.4985	76	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078195.1	s__Lachnoclostridium sp900078195	76.7857	66	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	76.7573	56	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCA_905214875.1	s__KM106-2 sp905214875	76.5035	51	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KM106-2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167115.1	s__Eubacterium_S uniforme	76.4464	61	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_S	95.0	97.48	97.33	0.80	0.75	5	-
GCF_018918265.1	s__Falcatimonas sp018918265	76.3836	60	917	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-28 18:28:09,433] [INFO] GTDB search result was written to GCA_015057455.1_ASM1505745v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:28:09,433] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:28:09,437] [INFO] DFAST_QC result json was written to GCA_015057455.1_ASM1505745v1_genomic.fna/dqc_result.json
[2023-06-28 18:28:09,438] [INFO] DFAST_QC completed!
[2023-06-28 18:28:09,438] [INFO] Total running time: 0h0m58s