[2024-01-25 18:51:05,971] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,974] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference
[2024-01-25 18:51:07,112] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:07,113] [INFO] Task started: Prodigal
[2024-01-25 18:51:07,113] [INFO] Running command: gunzip -c /var/lib/cwl/stg61ed6afe-2451-4b87-890b-0e92f594e767/GCF_000374345.1_ASM37434v1_genomic.fna.gz | prodigal -d GCF_000374345.1_ASM37434v1_genomic.fna/cds.fna -a GCF_000374345.1_ASM37434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:14,434] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:14,434] [INFO] Task started: HMMsearch
[2024-01-25 18:51:14,434] [INFO] Running command: hmmsearch --tblout GCF_000374345.1_ASM37434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference/reference_markers.hmm GCF_000374345.1_ASM37434v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:14,675] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:14,676] [INFO] Found 6/6 markers.
[2024-01-25 18:51:14,703] [INFO] Query marker FASTA was written to GCF_000374345.1_ASM37434v1_genomic.fna/markers.fasta
[2024-01-25 18:51:14,703] [INFO] Task started: Blastn
[2024-01-25 18:51:14,703] [INFO] Running command: blastn -query GCF_000374345.1_ASM37434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference/reference_markers.fasta -out GCF_000374345.1_ASM37434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:15,255] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:15,258] [INFO] Selected 17 target genomes.
[2024-01-25 18:51:15,258] [INFO] Target genome list was writen to GCF_000374345.1_ASM37434v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:15,273] [INFO] Task started: fastANI
[2024-01-25 18:51:15,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ed6afe-2451-4b87-890b-0e92f594e767/GCF_000374345.1_ASM37434v1_genomic.fna.gz --refList GCF_000374345.1_ASM37434v1_genomic.fna/target_genomes.txt --output GCF_000374345.1_ASM37434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:26,440] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:26,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:26,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:26,447] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:26,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:26,447] [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
Weizmannia acidiproducens	strain=DSM 23148	GCA_000374345.1	1121084	1121084	type	True	100.0	1056	1059	95	conclusive
Weizmannia coagulans	strain=ATCC 7050	GCA_000832905.1	1398	1398	suspected-type	True	78.7908	415	1059	95	below_threshold
Weizmannia coagulans	strain=DSM 1	GCA_000290615.1	1398	1398	suspected-type	True	78.7169	399	1059	95	below_threshold
Weizmannia coagulans	strain=DSM 1	GCA_900128875.1	1398	1398	suspected-type	True	78.6939	402	1059	95	below_threshold
Weizmannia coagulans	strain=ATCC 7050	GCA_000420205.1	1398	1398	suspected-type	True	78.6435	395	1059	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.6546	56	1059	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.2372	58	1059	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:26,448] [INFO] DFAST Taxonomy check result was written to GCF_000374345.1_ASM37434v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:26,450] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:26,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:26,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference/checkm_data
[2024-01-25 18:51:26,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:26,486] [INFO] Task started: CheckM
[2024-01-25 18:51:26,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000374345.1_ASM37434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000374345.1_ASM37434v1_genomic.fna/checkm_input GCF_000374345.1_ASM37434v1_genomic.fna/checkm_result
[2024-01-25 18:51:52,743] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:52,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:52,765] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:52,765] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:52,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000374345.1_ASM37434v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:52,766] [INFO] Task started: Blastn
[2024-01-25 18:51:52,766] [INFO] Running command: blastn -query GCF_000374345.1_ASM37434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b6dabb5-7ad0-475f-8507-73e241e68eca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000374345.1_ASM37434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:53,503] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:53,507] [INFO] Selected 25 target genomes.
[2024-01-25 18:51:53,507] [INFO] Target genome list was writen to GCF_000374345.1_ASM37434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:53,533] [INFO] Task started: fastANI
[2024-01-25 18:51:53,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg61ed6afe-2451-4b87-890b-0e92f594e767/GCF_000374345.1_ASM37434v1_genomic.fna.gz --refList GCF_000374345.1_ASM37434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000374345.1_ASM37434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:10,971] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:10,979] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:10,979] [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
GCF_000374345.1	s__Weizmannia acidiproducens	100.0	1056	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000169195.2	s__Weizmannia coagulans_A	79.0036	431	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	98.29	97.76	0.92	0.89	29	-
GCF_008974185.1	s__Weizmannia sp008974185	78.7304	460	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	99.76	99.74	0.95	0.95	3	-
GCF_000290615.1	s__Weizmannia coagulans	78.7132	400	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Weizmannia	95.0	98.84	97.70	0.92	0.87	18	-
GCF_003668575.1	s__Falsibacillus albus	76.6518	56	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-25281;g__Falsibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358205.1	s__Neobacillus salipaludis	76.4024	58	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860125.1	s__Bacillus_BJ canaveralius	76.3622	51	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	99.48	99.12	0.94	0.92	4	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	76.2309	51	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_001750285.1	s__Domibacillus iocasae	76.2223	52	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Domibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002860165.1	s__Bacillus_BJ sp002860165	76.1849	53	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Bacillus_BJ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656545.1	s__Neobacillus sp014656545	76.1679	57	1059	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:10,980] [INFO] GTDB search result was written to GCF_000374345.1_ASM37434v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:10,981] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:10,983] [INFO] DFAST_QC result json was written to GCF_000374345.1_ASM37434v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:10,983] [INFO] DFAST_QC completed!
[2024-01-25 18:52:10,983] [INFO] Total running time: 0h1m5s