[2024-01-24 13:49:45,508] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference
[2024-01-24 13:49:46,948] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,948] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,949] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2ab674c-7396-42b7-936c-be92e5b5da1d/GCF_000968055.1_ASM96805v1_genomic.fna.gz | prodigal -d GCF_000968055.1_ASM96805v1_genomic.fna/cds.fna -a GCF_000968055.1_ASM96805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:49,611] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:49,612] [INFO] Task started: HMMsearch
[2024-01-24 13:49:49,612] [INFO] Running command: hmmsearch --tblout GCF_000968055.1_ASM96805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference/reference_markers.hmm GCF_000968055.1_ASM96805v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:49,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:49,857] [INFO] Found 6/6 markers.
[2024-01-24 13:49:49,875] [INFO] Query marker FASTA was written to GCF_000968055.1_ASM96805v1_genomic.fna/markers.fasta
[2024-01-24 13:49:49,875] [INFO] Task started: Blastn
[2024-01-24 13:49:49,876] [INFO] Running command: blastn -query GCF_000968055.1_ASM96805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference/reference_markers.fasta -out GCF_000968055.1_ASM96805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:50,519] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:50,522] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:50,523] [INFO] Target genome list was writen to GCF_000968055.1_ASM96805v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:50,531] [INFO] Task started: fastANI
[2024-01-24 13:49:50,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2ab674c-7396-42b7-936c-be92e5b5da1d/GCF_000968055.1_ASM96805v1_genomic.fna.gz --refList GCF_000968055.1_ASM96805v1_genomic.fna/target_genomes.txt --output GCF_000968055.1_ASM96805v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,208] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:58,208] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,208] [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
Alteracholeplasma palmae	strain=J233	GCA_000968055.1	38986	38986	type	True	100.0	518	518	95	conclusive
Acholeplasma laidlawii	strain=NCTC10116	GCA_900476025.1	2148	2148	type	True	77.8006	53	518	95	below_threshold
Mariniplasma anaerobium	strain=Mahy22	GCA_016865445.1	2735436	2735436	type	True	77.769	62	518	95	below_threshold
Acholeplasma laidlawii	strain=PG-8A	GCA_000018785.1	2148	2148	type	True	77.4034	53	518	95	below_threshold
Haploplasma axanthum	strain=NCTC10138	GCA_900660745.1	29552	29552	type	True	77.3383	83	518	95	below_threshold
Haploplasma axanthum	strain=ATCC 25176	GCA_000428705.1	29552	29552	type	True	77.0165	80	518	95	below_threshold
Haploplasma modicum	strain=ATCC 29102	GCA_000687835.1	2150	2150	type	True	77.0009	59	518	95	below_threshold
Acholeplasma laidlawii	strain=DSM 23060	GCA_003385765.1	2148	2148	type	True	76.8943	50	518	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,210] [INFO] DFAST Taxonomy check result was written to GCF_000968055.1_ASM96805v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference/checkm_data
[2024-01-24 13:49:58,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,235] [INFO] Task started: CheckM
[2024-01-24 13:49:58,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000968055.1_ASM96805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000968055.1_ASM96805v1_genomic.fna/checkm_input GCF_000968055.1_ASM96805v1_genomic.fna/checkm_result
[2024-01-24 13:50:14,258] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:14,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:14,278] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:14,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:14,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000968055.1_ASM96805v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:14,279] [INFO] Task started: Blastn
[2024-01-24 13:50:14,279] [INFO] Running command: blastn -query GCF_000968055.1_ASM96805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41625f4b-b6df-436d-94c5-839faf39a672/dqc_reference/reference_markers_gtdb.fasta -out GCF_000968055.1_ASM96805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:15,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:15,264] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:15,265] [INFO] Target genome list was writen to GCF_000968055.1_ASM96805v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:15,281] [INFO] Task started: fastANI
[2024-01-24 13:50:15,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2ab674c-7396-42b7-936c-be92e5b5da1d/GCF_000968055.1_ASM96805v1_genomic.fna.gz --refList GCF_000968055.1_ASM96805v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000968055.1_ASM96805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:21,092] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:21,106] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:21,107] [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_000968055.1	s__Acholeplasma_D palmae	100.0	518	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012519065.1	s__Acholeplasma_D sp012519065	78.5482	103	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865445.1	s__MZ-XQ sp016865445	77.8357	60	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__MZ-XQ	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018785.1	s__Acholeplasma laidlawii	77.6739	51	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.83	98.26	1.00	1.00	15	-
GCF_000526235.1	s__Acholeplasma granularum	77.4548	59	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660745.1	s__Acholeplasma_A axanthum	77.167	80	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000687835.1	s__Acholeplasma_A modicum	76.9538	58	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709225.1	s__Acholeplasma laidlawii_A	76.8128	53	518	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,108] [INFO] GTDB search result was written to GCF_000968055.1_ASM96805v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:21,109] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:21,112] [INFO] DFAST_QC result json was written to GCF_000968055.1_ASM96805v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:21,112] [INFO] DFAST_QC completed!
[2024-01-24 13:50:21,112] [INFO] Total running time: 0h0m36s