[2023-06-13 01:25:14,560] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:25:14,563] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:25:14,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference
[2023-06-13 01:25:15,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:25:15,917] [INFO] Task started: Prodigal
[2023-06-13 01:25:15,918] [INFO] Running command: gunzip -c /var/lib/cwl/stgf70efd45-8fd8-4d37-822f-c139d092fadd/GCA_022764265.1_ASM2276426v1_genomic.fna.gz | prodigal -d GCA_022764265.1_ASM2276426v1_genomic.fna/cds.fna -a GCA_022764265.1_ASM2276426v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:25:21,333] [INFO] Task succeeded: Prodigal
[2023-06-13 01:25:21,333] [INFO] Task started: HMMsearch
[2023-06-13 01:25:21,333] [INFO] Running command: hmmsearch --tblout GCA_022764265.1_ASM2276426v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference/reference_markers.hmm GCA_022764265.1_ASM2276426v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:25:21,574] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:25:21,575] [INFO] Found 6/6 markers.
[2023-06-13 01:25:21,601] [INFO] Query marker FASTA was written to GCA_022764265.1_ASM2276426v1_genomic.fna/markers.fasta
[2023-06-13 01:25:21,601] [INFO] Task started: Blastn
[2023-06-13 01:25:21,602] [INFO] Running command: blastn -query GCA_022764265.1_ASM2276426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference/reference_markers.fasta -out GCA_022764265.1_ASM2276426v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:25:22,264] [INFO] Task succeeded: Blastn
[2023-06-13 01:25:22,269] [INFO] Selected 29 target genomes.
[2023-06-13 01:25:22,270] [INFO] Target genome list was writen to GCA_022764265.1_ASM2276426v1_genomic.fna/target_genomes.txt
[2023-06-13 01:25:22,273] [INFO] Task started: fastANI
[2023-06-13 01:25:22,273] [INFO] Running command: fastANI --query /var/lib/cwl/stgf70efd45-8fd8-4d37-822f-c139d092fadd/GCA_022764265.1_ASM2276426v1_genomic.fna.gz --refList GCA_022764265.1_ASM2276426v1_genomic.fna/target_genomes.txt --output GCA_022764265.1_ASM2276426v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:25:36,678] [INFO] Task succeeded: fastANI
[2023-06-13 01:25:36,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:25:36,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:25:36,686] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:25:36,687] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:25:36,687] [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
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	77.9948	159	701	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.4367	51	701	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:25:36,689] [INFO] DFAST Taxonomy check result was written to GCA_022764265.1_ASM2276426v1_genomic.fna/tc_result.tsv
[2023-06-13 01:25:36,689] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:25:36,690] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:25:36,690] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference/checkm_data
[2023-06-13 01:25:36,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:25:36,720] [INFO] Task started: CheckM
[2023-06-13 01:25:36,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022764265.1_ASM2276426v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022764265.1_ASM2276426v1_genomic.fna/checkm_input GCA_022764265.1_ASM2276426v1_genomic.fna/checkm_result
[2023-06-13 01:26:00,506] [INFO] Task succeeded: CheckM
[2023-06-13 01:26:00,508] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 01:26:00,529] [INFO] ===== Completeness check finished =====
[2023-06-13 01:26:00,530] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:26:00,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022764265.1_ASM2276426v1_genomic.fna/markers.fasta)
[2023-06-13 01:26:00,531] [INFO] Task started: Blastn
[2023-06-13 01:26:00,531] [INFO] Running command: blastn -query GCA_022764265.1_ASM2276426v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2ace6e1-c36c-4032-b351-05243f0ca618/dqc_reference/reference_markers_gtdb.fasta -out GCA_022764265.1_ASM2276426v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:26:01,669] [INFO] Task succeeded: Blastn
[2023-06-13 01:26:01,674] [INFO] Selected 18 target genomes.
[2023-06-13 01:26:01,675] [INFO] Target genome list was writen to GCA_022764265.1_ASM2276426v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:26:01,684] [INFO] Task started: fastANI
[2023-06-13 01:26:01,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgf70efd45-8fd8-4d37-822f-c139d092fadd/GCA_022764265.1_ASM2276426v1_genomic.fna.gz --refList GCA_022764265.1_ASM2276426v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022764265.1_ASM2276426v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:26:09,755] [INFO] Task succeeded: fastANI
[2023-06-13 01:26:09,770] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:26:09,771] [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_019113845.1	s__Anaerobutyricum avicola	78.2602	169	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161065.1	s__Anaerobutyricum faecale	78.2601	211	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.93	98.91	0.92	0.91	3	-
GCA_900016875.1	s__Anaerobutyricum stercoris	78.1678	212	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.34	98.09	0.89	0.78	6	-
GCF_000173975.1	s__Anaerobutyricum hallii	78.0178	158	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.51	97.99	0.84	0.63	21	-
GCF_900209925.1	s__Anaerobutyricum soehngenii	77.8812	162	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	97.18	96.91	0.82	0.70	12	-
GCA_900754855.1	s__Anaerobutyricum sp900754855	77.8018	122	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	99.80	99.80	0.88	0.88	2	-
GCA_019114885.1	s__Anaerobutyricum stercoripullorum	77.2887	125	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	97.84	97.84	0.89	0.89	2	-
GCA_017433295.1	s__Anaerobutyricum sp017433295	76.8294	75	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902796415.1	s__Anaerobutyricum sp902796415	75.8892	52	701	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:26:09,773] [INFO] GTDB search result was written to GCA_022764265.1_ASM2276426v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:26:09,773] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:26:09,779] [INFO] DFAST_QC result json was written to GCA_022764265.1_ASM2276426v1_genomic.fna/dqc_result.json
[2023-06-13 01:26:09,779] [INFO] DFAST_QC completed!
[2023-06-13 01:26:09,779] [INFO] Total running time: 0h0m55s