[2024-01-24 13:49:42,866] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:42,869] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:42,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference
[2024-01-24 13:49:44,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:44,113] [INFO] Task started: Prodigal
[2024-01-24 13:49:44,114] [INFO] Running command: gunzip -c /var/lib/cwl/stgabdf6883-9555-4b9d-81b4-3fa900102cbf/GCF_004358345.1_ASM435834v1_genomic.fna.gz | prodigal -d GCF_004358345.1_ASM435834v1_genomic.fna/cds.fna -a GCF_004358345.1_ASM435834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:56,553] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:56,553] [INFO] Task started: HMMsearch
[2024-01-24 13:49:56,553] [INFO] Running command: hmmsearch --tblout GCF_004358345.1_ASM435834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference/reference_markers.hmm GCF_004358345.1_ASM435834v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:56,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:56,876] [INFO] Found 6/6 markers.
[2024-01-24 13:49:56,918] [INFO] Query marker FASTA was written to GCF_004358345.1_ASM435834v1_genomic.fna/markers.fasta
[2024-01-24 13:49:56,918] [INFO] Task started: Blastn
[2024-01-24 13:49:56,918] [INFO] Running command: blastn -query GCF_004358345.1_ASM435834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference/reference_markers.fasta -out GCF_004358345.1_ASM435834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,655] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,659] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:57,660] [INFO] Target genome list was writen to GCF_004358345.1_ASM435834v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:57,666] [INFO] Task started: fastANI
[2024-01-24 13:49:57,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgabdf6883-9555-4b9d-81b4-3fa900102cbf/GCF_004358345.1_ASM435834v1_genomic.fna.gz --refList GCF_004358345.1_ASM435834v1_genomic.fna/target_genomes.txt --output GCF_004358345.1_ASM435834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:07,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:07,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:07,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:07,280] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:51:07,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:51:07,281] [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
Parashewanella spongiae	strain=HJ039	GCA_004358345.1	342950	342950	type	True	100.0	1821	1822	95	conclusive
Parashewanella spongiae	strain=KCTC 22492	GCA_003676335.1	342950	342950	type	True	99.8506	1490	1822	95	conclusive
Parashewanella spongiae	strain=KCTC 22492	GCA_023283745.1	342950	342950	type	True	99.8178	1466	1822	95	conclusive
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	78.6354	320	1822	95	below_threshold
Parashewanella tropica	strain=MEBiC05444	GCA_004358445.1	2547970	2547970	type	True	78.551	250	1822	95	below_threshold
Shewanella marina	strain=JCM 15074	GCA_000614975.1	487319	487319	type	True	78.4236	110	1822	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.2248	114	1822	95	below_threshold
Parashewanella curva	strain=C51	GCA_003675895.1	2338552	2338552	type	True	78.2059	258	1822	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	77.9491	131	1822	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	77.8336	137	1822	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	77.6244	133	1822	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	77.5218	132	1822	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	76.573	55	1822	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	76.3104	51	1822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:07,282] [INFO] DFAST Taxonomy check result was written to GCF_004358345.1_ASM435834v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:07,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:07,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:07,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference/checkm_data
[2024-01-24 13:51:07,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:07,335] [INFO] Task started: CheckM
[2024-01-24 13:51:07,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358345.1_ASM435834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358345.1_ASM435834v1_genomic.fna/checkm_input GCF_004358345.1_ASM435834v1_genomic.fna/checkm_result
[2024-01-24 13:51:45,619] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:45,620] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:45,640] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:45,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:45,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358345.1_ASM435834v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:45,641] [INFO] Task started: Blastn
[2024-01-24 13:51:45,641] [INFO] Running command: blastn -query GCF_004358345.1_ASM435834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c6d91d1-74e8-4aad-ba07-32ec98f4c862/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358345.1_ASM435834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:46,753] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:46,757] [INFO] Selected 18 target genomes.
[2024-01-24 13:51:46,757] [INFO] Target genome list was writen to GCF_004358345.1_ASM435834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:46,801] [INFO] Task started: fastANI
[2024-01-24 13:51:46,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgabdf6883-9555-4b9d-81b4-3fa900102cbf/GCF_004358345.1_ASM435834v1_genomic.fna.gz --refList GCF_004358345.1_ASM435834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358345.1_ASM435834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:25,154] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:25,175] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:25,176] [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_004358345.1	s__Parashewanella spongiae	100.0	1821	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000019525.1	s__Shewanella woodyi	79.4763	119	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.96	97.96	0.94	0.94	2	-
GCF_000013765.1	s__Shewanella denitrificans	79.4368	123	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456975.1	s__Shewanella baltica	79.3787	151	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_000019185.1	s__Shewanella halifaxensis	79.2566	132	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	78.8802	161	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	78.7749	155	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_016900895.1	s__Parashewanella sp016900895	78.7112	313	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011765625.1	s__Shewanella aestuarii_A	78.5877	161	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358445.1	s__Parashewanella tropica	78.5235	248	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168585.1	s__Parashewanella sp004168585	78.4817	285	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018221465.1	s__Shewanella intestini	78.4478	132	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000614975.1	s__Shewanella marina	78.422	108	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675895.1	s__Parashewanella curva	78.2574	251	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	78.0609	149	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_014656435.1	s__Thalassotalea_C marina	76.545	53	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	76.3437	50	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378355.1	s__Psychromonas sp004378355	76.1428	50	1822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:25,177] [INFO] GTDB search result was written to GCF_004358345.1_ASM435834v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:25,178] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:25,182] [INFO] DFAST_QC result json was written to GCF_004358345.1_ASM435834v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:25,182] [INFO] DFAST_QC completed!
[2024-01-24 13:52:25,182] [INFO] Total running time: 0h2m42s