[2023-06-28 18:56:11,352] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:56:11,359] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:56:11,359] [INFO] DQC Reference Directory: /var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference
[2023-06-28 18:56:12,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:56:12,964] [INFO] Task started: Prodigal
[2023-06-28 18:56:12,964] [INFO] Running command: gunzip -c /var/lib/cwl/stge2597029-03c5-4702-99ff-1f4543360379/GCA_020628185.1_ASM2062818v1_genomic.fna.gz | prodigal -d GCA_020628185.1_ASM2062818v1_genomic.fna/cds.fna -a GCA_020628185.1_ASM2062818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:56:20,413] [INFO] Task succeeded: Prodigal
[2023-06-28 18:56:20,413] [INFO] Task started: HMMsearch
[2023-06-28 18:56:20,413] [INFO] Running command: hmmsearch --tblout GCA_020628185.1_ASM2062818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference/reference_markers.hmm GCA_020628185.1_ASM2062818v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:56:20,717] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:56:20,718] [INFO] Found 6/6 markers.
[2023-06-28 18:56:20,771] [INFO] Query marker FASTA was written to GCA_020628185.1_ASM2062818v1_genomic.fna/markers.fasta
[2023-06-28 18:56:20,771] [INFO] Task started: Blastn
[2023-06-28 18:56:20,772] [INFO] Running command: blastn -query GCA_020628185.1_ASM2062818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference/reference_markers.fasta -out GCA_020628185.1_ASM2062818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:56:21,540] [INFO] Task succeeded: Blastn
[2023-06-28 18:56:21,547] [INFO] Selected 15 target genomes.
[2023-06-28 18:56:21,547] [INFO] Target genome list was writen to GCA_020628185.1_ASM2062818v1_genomic.fna/target_genomes.txt
[2023-06-28 18:56:21,555] [INFO] Task started: fastANI
[2023-06-28 18:56:21,555] [INFO] Running command: fastANI --query /var/lib/cwl/stge2597029-03c5-4702-99ff-1f4543360379/GCA_020628185.1_ASM2062818v1_genomic.fna.gz --refList GCA_020628185.1_ASM2062818v1_genomic.fna/target_genomes.txt --output GCA_020628185.1_ASM2062818v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:56:33,937] [INFO] Task succeeded: fastANI
[2023-06-28 18:56:33,937] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:56:33,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:56:33,951] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 18:56:33,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 18:56:33,951] [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
Pseudoalteromonas marina	strain=DSM 17587	GCA_000238335.4	267375	267375	type	True	97.9226	1156	1305	95	conclusive
Pseudoalteromonas carrageenovora	strain=ATCC 43555	GCA_900239935.1	227	227	type	True	84.0262	894	1305	95	below_threshold
Pseudoalteromonas carrageenovora	strain=NBRC 12985	GCA_006539245.1	227	227	type	True	84.0221	861	1305	95	below_threshold
Pseudoalteromonas carrageenovora	strain=IAM 12662	GCA_014925295.1	227	227	type	True	83.9694	896	1305	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	83.4387	808	1305	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	82.7171	828	1305	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	82.6871	884	1305	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	81.1138	667	1305	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	81.1054	689	1305	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KMM 3549	GCA_002310795.1	152297	152297	suspected-type	True	81.0516	704	1305	95	below_threshold
Pseudoalteromonas issachenkonii	strain=KCTC 12958	GCA_001455325.1	152297	152297	suspected-type	True	81.0154	711	1305	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	76.2631	51	1305	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.0353	52	1305	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	75.9127	60	1305	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:56:33,953] [INFO] DFAST Taxonomy check result was written to GCA_020628185.1_ASM2062818v1_genomic.fna/tc_result.tsv
[2023-06-28 18:56:33,954] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:56:33,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:56:33,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference/checkm_data
[2023-06-28 18:56:33,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:56:34,002] [INFO] Task started: CheckM
[2023-06-28 18:56:34,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020628185.1_ASM2062818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020628185.1_ASM2062818v1_genomic.fna/checkm_input GCA_020628185.1_ASM2062818v1_genomic.fna/checkm_result
[2023-06-28 18:57:02,539] [INFO] Task succeeded: CheckM
[2023-06-28 18:57:02,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:57:02,561] [INFO] ===== Completeness check finished =====
[2023-06-28 18:57:02,562] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:57:02,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020628185.1_ASM2062818v1_genomic.fna/markers.fasta)
[2023-06-28 18:57:02,563] [INFO] Task started: Blastn
[2023-06-28 18:57:02,563] [INFO] Running command: blastn -query GCA_020628185.1_ASM2062818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b3e7c1-0d21-4d83-a191-44286aa8785e/dqc_reference/reference_markers_gtdb.fasta -out GCA_020628185.1_ASM2062818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:57:03,688] [INFO] Task succeeded: Blastn
[2023-06-28 18:57:03,725] [INFO] Selected 13 target genomes.
[2023-06-28 18:57:03,726] [INFO] Target genome list was writen to GCA_020628185.1_ASM2062818v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:57:03,737] [INFO] Task started: fastANI
[2023-06-28 18:57:03,737] [INFO] Running command: fastANI --query /var/lib/cwl/stge2597029-03c5-4702-99ff-1f4543360379/GCA_020628185.1_ASM2062818v1_genomic.fna.gz --refList GCA_020628185.1_ASM2062818v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020628185.1_ASM2062818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:57:15,523] [INFO] Task succeeded: fastANI
[2023-06-28 18:57:15,539] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:57:15,539] [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_000238335.3	s__Pseudoalteromonas marina	97.9226	1156	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	conclusive
GCF_001468485.1	s__Pseudoalteromonas sp001468485	91.4878	1085	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.31	96.95	0.95	0.92	8	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	84.0155	895	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	83.4696	813	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	83.4016	819	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	82.7135	829	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	82.5382	908	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	82.5259	858	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238395.3	s__Pseudoalteromonas arctica	82.4971	870	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	81.3515	664	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_000238275.3	s__Pseudoalteromonas undina	81.2359	690	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	81.1055	689	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	80.7387	661	1305	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:57:15,541] [INFO] GTDB search result was written to GCA_020628185.1_ASM2062818v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:57:15,542] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:57:15,548] [INFO] DFAST_QC result json was written to GCA_020628185.1_ASM2062818v1_genomic.fna/dqc_result.json
[2023-06-28 18:57:15,548] [INFO] DFAST_QC completed!
[2023-06-28 18:57:15,549] [INFO] Total running time: 0h1m4s