[2024-01-24 13:48:59,635] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,637] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,637] [INFO] DQC Reference Directory: /var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference
[2024-01-24 13:49:00,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:00,981] [INFO] Task started: Prodigal
[2024-01-24 13:49:00,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg2df0a674-207a-4083-a46a-3f45ebebcc50/GCF_003385765.1_ASM338576v1_genomic.fna.gz | prodigal -d GCF_003385765.1_ASM338576v1_genomic.fna/cds.fna -a GCF_003385765.1_ASM338576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:03,569] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:03,569] [INFO] Task started: HMMsearch
[2024-01-24 13:49:03,569] [INFO] Running command: hmmsearch --tblout GCF_003385765.1_ASM338576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference/reference_markers.hmm GCF_003385765.1_ASM338576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:03,831] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:03,833] [INFO] Found 6/6 markers.
[2024-01-24 13:49:03,852] [INFO] Query marker FASTA was written to GCF_003385765.1_ASM338576v1_genomic.fna/markers.fasta
[2024-01-24 13:49:03,853] [INFO] Task started: Blastn
[2024-01-24 13:49:03,853] [INFO] Running command: blastn -query GCF_003385765.1_ASM338576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference/reference_markers.fasta -out GCF_003385765.1_ASM338576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:04,466] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:04,469] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:04,469] [INFO] Target genome list was writen to GCF_003385765.1_ASM338576v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:04,538] [INFO] Task started: fastANI
[2024-01-24 13:49:04,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df0a674-207a-4083-a46a-3f45ebebcc50/GCF_003385765.1_ASM338576v1_genomic.fna.gz --refList GCF_003385765.1_ASM338576v1_genomic.fna/target_genomes.txt --output GCF_003385765.1_ASM338576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:09,092] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:09,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:09,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:09,106] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:49:09,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:09,106] [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
Acholeplasma laidlawii	strain=DSM 23060	GCA_003385765.1	2148	2148	type	True	100.0	496	496	95	conclusive
Acholeplasma laidlawii	strain=NCTC10116	GCA_900476025.1	2148	2148	type	True	99.9953	495	496	95	conclusive
Acholeplasma laidlawii	strain=PG-8A	GCA_000018785.1	2148	2148	type	True	99.988	496	496	95	conclusive
Acholeplasma granularum	strain=ATCC 19168	GCA_000526235.1	264635	264635	type	True	80.3781	228	496	95	below_threshold
Acholeplasma oculi	strain=NCTC10150	GCA_900444665.1	35623	35623	type	True	78.8841	176	496	95	below_threshold
Acholeplasma oculi	strain=ATCC 27350	GCA_900166985.1	35623	35623	type	True	78.8213	176	496	95	below_threshold
Acholeplasma equifetale	strain=ATCC 29724	GCA_000687735.1	264634	264634	type	True	77.5014	90	496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:09,108] [INFO] DFAST Taxonomy check result was written to GCF_003385765.1_ASM338576v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:09,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:09,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:09,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference/checkm_data
[2024-01-24 13:49:09,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:09,131] [INFO] Task started: CheckM
[2024-01-24 13:49:09,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385765.1_ASM338576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385765.1_ASM338576v1_genomic.fna/checkm_input GCF_003385765.1_ASM338576v1_genomic.fna/checkm_result
[2024-01-24 13:49:25,210] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:25,212] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:25,233] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:25,233] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:25,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385765.1_ASM338576v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:25,234] [INFO] Task started: Blastn
[2024-01-24 13:49:25,234] [INFO] Running command: blastn -query GCF_003385765.1_ASM338576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91f01351-5714-4790-a983-435bb566d551/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385765.1_ASM338576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:26,233] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:26,238] [INFO] Selected 10 target genomes.
[2024-01-24 13:49:26,239] [INFO] Target genome list was writen to GCF_003385765.1_ASM338576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:26,317] [INFO] Task started: fastANI
[2024-01-24 13:49:26,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df0a674-207a-4083-a46a-3f45ebebcc50/GCF_003385765.1_ASM338576v1_genomic.fna.gz --refList GCF_003385765.1_ASM338576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385765.1_ASM338576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:29,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:29,175] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:29,175] [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_000018785.1	s__Acholeplasma laidlawii	99.988	496	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.83	98.26	1.00	1.00	15	conclusive
GCF_015709225.1	s__Acholeplasma laidlawii_A	93.2222	375	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526235.1	s__Acholeplasma granularum	80.3781	228	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399815.1	s__Acholeplasma sp002399815	78.886	163	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166985.1	s__Acholeplasma oculi	78.8213	176	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900660755.1	s__Acholeplasma hippikon	77.7256	110	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017052655.1	s__Acholeplasma equirhinis	77.6913	127	496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687735.1	s__Acholeplasma equifetale	77.5014	90	496	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 13:49:29,176] [INFO] GTDB search result was written to GCF_003385765.1_ASM338576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:29,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:29,179] [INFO] DFAST_QC result json was written to GCF_003385765.1_ASM338576v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:29,180] [INFO] DFAST_QC completed!
[2024-01-24 13:49:29,180] [INFO] Total running time: 0h0m30s