[2023-03-17 07:28:31,302] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,333] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference
[2023-03-17 07:28:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stg17cccccf-223e-4c9d-a573-bd28d7cfa99c/OceanDNA-b13452.fa | prodigal -d OceanDNA-b13452/cds.fna -a OceanDNA-b13452/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:43,855] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:43,855] [INFO] Task started: HMMsearch
[2023-03-17 07:28:43,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b13452/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference/reference_markers.hmm OceanDNA-b13452/protein.faa > /dev/null
[2023-03-17 07:28:44,055] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:44,056] [INFO] Found 6/6 markers.
[2023-03-17 07:28:44,071] [INFO] Query marker FASTA was written to OceanDNA-b13452/markers.fasta
[2023-03-17 07:28:44,071] [INFO] Task started: Blastn
[2023-03-17 07:28:44,071] [INFO] Running command: blastn -query OceanDNA-b13452/markers.fasta -db /var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference/reference_markers.fasta -out OceanDNA-b13452/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:44,625] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:44,626] [INFO] Selected 17 target genomes.
[2023-03-17 07:28:44,626] [INFO] Target genome list was writen to OceanDNA-b13452/target_genomes.txt
[2023-03-17 07:28:44,635] [INFO] Task started: fastANI
[2023-03-17 07:28:44,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg17cccccf-223e-4c9d-a573-bd28d7cfa99c/OceanDNA-b13452.fa --refList OceanDNA-b13452/target_genomes.txt --output OceanDNA-b13452/fastani_result.tsv --threads 1
[2023-03-17 07:28:51,002] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:51,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:51,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:51,010] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:51,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:28:51,010] [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
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.3279	170	699	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.2296	201	699	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.1822	194	699	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.9412	160	699	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.8904	161	699	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	77.8171	109	699	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	77.7255	117	699	95	below_threshold
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.6832	154	699	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.611	127	699	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	77.5808	118	699	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.0939	111	699	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	76.973	112	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:28:51,010] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13452/tc_result.tsv
[2023-03-17 07:28:51,011] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:51,011] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:51,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference/checkm_data
[2023-03-17 07:28:51,011] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:51,015] [INFO] Task started: CheckM
[2023-03-17 07:28:51,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13452/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13452/checkm_input OceanDNA-b13452/checkm_result
[2023-03-17 07:29:21,673] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:21,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:21,676] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:21,676] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:21,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13452/markers.fasta)
[2023-03-17 07:29:21,676] [INFO] Task started: Blastn
[2023-03-17 07:29:21,676] [INFO] Running command: blastn -query OceanDNA-b13452/markers.fasta -db /var/lib/cwl/stg054823cc-bb30-4c78-861b-deac6feb2c82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13452/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:22,420] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:22,420] [INFO] Selected 14 target genomes.
[2023-03-17 07:29:22,420] [INFO] Target genome list was writen to OceanDNA-b13452/target_genomes_gtdb.txt
[2023-03-17 07:29:22,610] [INFO] Task started: fastANI
[2023-03-17 07:29:22,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg17cccccf-223e-4c9d-a573-bd28d7cfa99c/OceanDNA-b13452.fa --refList OceanDNA-b13452/target_genomes_gtdb.txt --output OceanDNA-b13452/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:28,526] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:28,535] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:29:28,535] [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_018698455.1	s__Sulfurimonas sp018698455	99.965	677	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002335055.1	s__Sulfurimonas sp002335055	80.0516	253	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	-
GCF_017357825.1	s__Sulfurimonas sp017357825	79.582	287	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733945.2	s__Sulfurimonas sp002733945	79.454	270	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015663215.1	s__Sulfurimonas sp015663215	79.2026	180	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978465.1	s__Sulfurimonas sp003978465	79.169	213	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744025.1	s__Sulfurimonas sp016744025	78.6574	181	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488615.1	s__Sulfurimonas sp015488615	78.6537	196	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCA_014381585.1	s__Sulfurimonas ponti	78.2153	167	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_015487435.1	s__Sulfurimonas sp015487435	78.0954	146	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938175.1	s__Sulfurimonas sp016938175	78.002	177	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016735225.1	s__Sulfurimonas sp016735225	77.7661	120	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013791885.1	s__Sulfurimonas sp013791885	77.7083	134	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	98.60	0.95	0.92	8	-
GCA_002733155.1	s__Sulfurimonas sp002733155	77.6467	140	699	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:28,535] [INFO] GTDB search result was written to OceanDNA-b13452/result_gtdb.tsv
[2023-03-17 07:29:28,535] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:28,537] [INFO] DFAST_QC result json was written to OceanDNA-b13452/dqc_result.json
[2023-03-17 07:29:28,537] [INFO] DFAST_QC completed!
[2023-03-17 07:29:28,537] [INFO] Total running time: 0h0m57s