[2024-01-24 11:36:20,753] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:20,755] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:20,755] [INFO] DQC Reference Directory: /var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference
[2024-01-24 11:36:21,990] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:21,991] [INFO] Task started: Prodigal
[2024-01-24 11:36:21,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c55a359-ddbf-4018-9ec9-a0a225f279a1/GCF_016132445.1_ASM1613244v1_genomic.fna.gz | prodigal -d GCF_016132445.1_ASM1613244v1_genomic.fna/cds.fna -a GCF_016132445.1_ASM1613244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:30,236] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:30,237] [INFO] Task started: HMMsearch
[2024-01-24 11:36:30,237] [INFO] Running command: hmmsearch --tblout GCF_016132445.1_ASM1613244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference/reference_markers.hmm GCF_016132445.1_ASM1613244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:30,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:30,478] [INFO] Found 6/6 markers.
[2024-01-24 11:36:30,508] [INFO] Query marker FASTA was written to GCF_016132445.1_ASM1613244v1_genomic.fna/markers.fasta
[2024-01-24 11:36:30,508] [INFO] Task started: Blastn
[2024-01-24 11:36:30,509] [INFO] Running command: blastn -query GCF_016132445.1_ASM1613244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference/reference_markers.fasta -out GCF_016132445.1_ASM1613244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:31,349] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:31,353] [INFO] Selected 22 target genomes.
[2024-01-24 11:36:31,353] [INFO] Target genome list was writen to GCF_016132445.1_ASM1613244v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:31,426] [INFO] Task started: fastANI
[2024-01-24 11:36:31,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c55a359-ddbf-4018-9ec9-a0a225f279a1/GCF_016132445.1_ASM1613244v1_genomic.fna.gz --refList GCF_016132445.1_ASM1613244v1_genomic.fna/target_genomes.txt --output GCF_016132445.1_ASM1613244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:46,196] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:46,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:46,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:46,218] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:36:46,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:36:46,218] [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
Thalassolituus marinus	strain=IMCC1826	GCA_020320395.1	671053	671053	type	True	79.4174	391	942	95	below_threshold
Oleibacter marinus	strain=DSM 24913	GCA_900156675.1	484498	484498	type	True	78.3052	171	942	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	78.1106	229	942	95	below_threshold
Oceanobacter kriegii	strain=DSM 6294	GCA_000422845.1	64972	64972	type	True	77.7734	262	942	95	below_threshold
Bacterioplanes sanyensis	strain=KCTC 32220	GCA_014652515.1	1249553	1249553	type	True	77.5351	223	942	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	77.3888	81	942	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	77.286	79	942	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	77.2358	105	942	95	below_threshold
Pseudomonas eucalypticola	strain=NP-1	GCA_013374995.1	2599595	2599595	type	True	77.2232	97	942	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.0546	108	942	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.9168	98	942	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	76.8465	87	942	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.7945	88	942	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.7516	57	942	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	76.5834	89	942	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	76.4389	103	942	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	76.3604	95	942	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	76.2781	103	942	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	76.2576	75	942	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.2312	91	942	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.2126	55	942	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	75.934	78	942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:46,228] [INFO] DFAST Taxonomy check result was written to GCF_016132445.1_ASM1613244v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:46,228] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:46,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:46,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference/checkm_data
[2024-01-24 11:36:46,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:46,265] [INFO] Task started: CheckM
[2024-01-24 11:36:46,265] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016132445.1_ASM1613244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016132445.1_ASM1613244v1_genomic.fna/checkm_input GCF_016132445.1_ASM1613244v1_genomic.fna/checkm_result
[2024-01-24 11:37:15,486] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:15,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:15,508] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:15,509] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:15,509] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016132445.1_ASM1613244v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:15,509] [INFO] Task started: Blastn
[2024-01-24 11:37:15,510] [INFO] Running command: blastn -query GCF_016132445.1_ASM1613244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6099c5e-660f-4e67-9450-6d86979de722/dqc_reference/reference_markers_gtdb.fasta -out GCF_016132445.1_ASM1613244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:16,900] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:16,905] [INFO] Selected 9 target genomes.
[2024-01-24 11:37:16,905] [INFO] Target genome list was writen to GCF_016132445.1_ASM1613244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:16,915] [INFO] Task started: fastANI
[2024-01-24 11:37:16,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c55a359-ddbf-4018-9ec9-a0a225f279a1/GCF_016132445.1_ASM1613244v1_genomic.fna.gz --refList GCF_016132445.1_ASM1613244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016132445.1_ASM1613244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:24,720] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:24,731] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:24,731] [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_016132445.1	s__UBA2009 sp016132445	100.0	941	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.98	97.98	0.94	0.94	2	conclusive
GCF_007785795.1	s__UBA2009 sp002335285	80.0292	558	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	97.54	97.44	0.92	0.92	6	-
GCA_002733205.1	s__UBA2009 sp002733205	79.6781	478	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	96.83	96.83	0.84	0.84	2	-
GCA_002314145.1	s__UBA2009 sp002314145	78.732	362	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	99.98	99.96	0.95	0.88	5	-
GCA_002706025.1	s__UBA2009 sp002706025	78.7275	360	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__UBA2009	95.0	98.78	97.86	0.91	0.85	7	-
GCF_900156675.1	s__Oleibacter marinus	78.3278	170	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.96	98.96	0.99	0.99	2	-
GCA_002724925.1	s__Oleibacter sp002724925	78.158	174	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	98.64	97.85	0.94	0.89	5	-
GCF_000422845.1	s__Oceanobacter kriegii	77.8463	256	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oceanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006212115.1	s__Oleibacter sp006212115	76.8757	137	942	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-6294;g__Oleibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:24,733] [INFO] GTDB search result was written to GCF_016132445.1_ASM1613244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:24,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:24,737] [INFO] DFAST_QC result json was written to GCF_016132445.1_ASM1613244v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:24,737] [INFO] DFAST_QC completed!
[2024-01-24 11:37:24,737] [INFO] Total running time: 0h1m4s