[2024-01-24 14:23:19,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:19,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:19,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference
[2024-01-24 14:23:20,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:20,542] [INFO] Task started: Prodigal
[2024-01-24 14:23:20,543] [INFO] Running command: gunzip -c /var/lib/cwl/stgb143ee1b-f41e-4cc1-90c0-8831e519cb2d/GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna.gz | prodigal -d GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/cds.fna -a GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:32,349] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:32,350] [INFO] Task started: HMMsearch
[2024-01-24 14:23:32,350] [INFO] Running command: hmmsearch --tblout GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference/reference_markers.hmm GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:32,737] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:32,738] [INFO] Found 6/6 markers.
[2024-01-24 14:23:32,779] [INFO] Query marker FASTA was written to GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/markers.fasta
[2024-01-24 14:23:32,779] [INFO] Task started: Blastn
[2024-01-24 14:23:32,779] [INFO] Running command: blastn -query GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference/reference_markers.fasta -out GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:33,858] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:33,862] [INFO] Selected 23 target genomes.
[2024-01-24 14:23:33,862] [INFO] Target genome list was writen to GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:33,872] [INFO] Task started: fastANI
[2024-01-24 14:23:33,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgb143ee1b-f41e-4cc1-90c0-8831e519cb2d/GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna.gz --refList GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/target_genomes.txt --output GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:52,737] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:52,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:52,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:52,754] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:52,754] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:52,755] [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
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	84.6538	860	1113	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	84.6235	872	1113	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	82.92	800	1113	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	79.6891	454	1113	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.6359	453	1113	95	below_threshold
Pseudomonas jinjuensis	strain=NBRC 103047	GCA_002091655.1	198616	198616	type	True	79.5913	443	1113	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	79.5733	471	1113	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	79.5057	446	1113	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	79.5041	486	1113	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	79.4652	439	1113	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	79.1967	452	1113	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	79.1197	466	1113	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.9931	416	1113	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.8659	428	1113	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	78.7285	426	1113	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	78.6386	381	1113	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	78.5711	387	1113	95	below_threshold
Pseudomonas batumici	strain=UCM B-321	GCA_000820515.1	226910	226910	type	True	78.398	354	1113	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	77.7616	282	1113	95	below_threshold
Pseudomonas quercus	strain=hsmgli-8	GCA_012033695.1	2722792	2722792	type	True	77.4864	191	1113	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	77.4778	142	1113	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	77.438	108	1113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:52,756] [INFO] DFAST Taxonomy check result was written to GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:52,757] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:52,757] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:52,757] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference/checkm_data
[2024-01-24 14:23:52,758] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:52,792] [INFO] Task started: CheckM
[2024-01-24 14:23:52,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/checkm_input GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/checkm_result
[2024-01-24 14:24:30,362] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:30,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:30,383] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:30,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:30,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 14:24:30,384] [INFO] Task started: Blastn
[2024-01-24 14:24:30,384] [INFO] Running command: blastn -query GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4afd3baa-0d0a-48d2-9b89-e6727a68e90b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:31,926] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:31,931] [INFO] Selected 9 target genomes.
[2024-01-24 14:24:31,931] [INFO] Target genome list was writen to GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:31,937] [INFO] Task started: fastANI
[2024-01-24 14:24:31,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgb143ee1b-f41e-4cc1-90c0-8831e519cb2d/GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna.gz --refList GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:39,106] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:39,115] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:39,115] [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_000939975.1	s__Pseudomonas_D saudimassiliensis	100.0	1113	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_019116555.1	s__Pseudomonas_D excrementavium	84.9446	687	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	84.6328	871	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	83.4294	797	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	83.338	797	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105005.1	s__Pseudomonas_D litoralis	82.9608	801	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012735335.1	s__Pseudomonas_D sp012735335	82.1616	502	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012033695.1	s__Pseudomonas_E quercus	77.4824	192	1113	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:39,117] [INFO] GTDB search result was written to GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:39,117] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:39,136] [INFO] DFAST_QC result json was written to GCF_000939975.1_PRJEB5504_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 14:24:39,137] [INFO] DFAST_QC completed!
[2024-01-24 14:24:39,137] [INFO] Total running time: 0h1m20s