[2023-03-15 14:37:49,312] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:37:49,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:37:49,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference
[2023-03-15 14:37:50,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:37:50,420] [INFO] Task started: Prodigal
[2023-03-15 14:37:50,420] [INFO] Running command: cat /var/lib/cwl/stg3dd77803-4967-44a7-b55c-b7713ab39fe2/OceanDNA-b13482.fa | prodigal -d OceanDNA-b13482/cds.fna -a OceanDNA-b13482/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:37:55,016] [INFO] Task succeeded: Prodigal
[2023-03-15 14:37:55,017] [INFO] Task started: HMMsearch
[2023-03-15 14:37:55,017] [INFO] Running command: hmmsearch --tblout OceanDNA-b13482/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference/reference_markers.hmm OceanDNA-b13482/protein.faa > /dev/null
[2023-03-15 14:37:55,163] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:37:55,164] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3dd77803-4967-44a7-b55c-b7713ab39fe2/OceanDNA-b13482.fa]
[2023-03-15 14:37:55,174] [INFO] Query marker FASTA was written to OceanDNA-b13482/markers.fasta
[2023-03-15 14:37:55,175] [INFO] Task started: Blastn
[2023-03-15 14:37:55,176] [INFO] Running command: blastn -query OceanDNA-b13482/markers.fasta -db /var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference/reference_markers.fasta -out OceanDNA-b13482/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:37:55,801] [INFO] Task succeeded: Blastn
[2023-03-15 14:37:55,802] [INFO] Selected 12 target genomes.
[2023-03-15 14:37:55,802] [INFO] Target genome list was writen to OceanDNA-b13482/target_genomes.txt
[2023-03-15 14:37:55,815] [INFO] Task started: fastANI
[2023-03-15 14:37:55,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd77803-4967-44a7-b55c-b7713ab39fe2/OceanDNA-b13482.fa --refList OceanDNA-b13482/target_genomes.txt --output OceanDNA-b13482/fastani_result.tsv --threads 1
[2023-03-15 14:37:59,959] [INFO] Task succeeded: fastANI
[2023-03-15 14:37:59,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:37:59,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:38:00,015] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:38:00,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:38:00,015] [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
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	77.4877	98	294	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.3885	108	294	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	77.3608	111	294	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.3358	91	294	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	77.199	66	294	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.0368	94	294	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.0063	68	294	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	76.9769	70	294	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	76.8473	63	294	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	76.6289	71	294	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:38:00,015] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13482/tc_result.tsv
[2023-03-15 14:38:00,016] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:38:00,016] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:38:00,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference/checkm_data
[2023-03-15 14:38:00,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:38:00,488] [INFO] Task started: CheckM
[2023-03-15 14:38:00,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13482/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13482/checkm_input OceanDNA-b13482/checkm_result
[2023-03-15 14:38:21,698] [INFO] Task succeeded: CheckM
[2023-03-15 14:38:21,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:38:21,714] [INFO] ===== Completeness check finished =====
[2023-03-15 14:38:21,714] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:38:21,714] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13482/markers.fasta)
[2023-03-15 14:38:21,716] [INFO] Task started: Blastn
[2023-03-15 14:38:21,716] [INFO] Running command: blastn -query OceanDNA-b13482/markers.fasta -db /var/lib/cwl/stg0ed1df32-ddca-4feb-a850-c494e22e1bcc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13482/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:22,593] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:22,594] [INFO] Selected 9 target genomes.
[2023-03-15 14:38:22,594] [INFO] Target genome list was writen to OceanDNA-b13482/target_genomes_gtdb.txt
[2023-03-15 14:38:22,606] [INFO] Task started: fastANI
[2023-03-15 14:38:22,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dd77803-4967-44a7-b55c-b7713ab39fe2/OceanDNA-b13482.fa --refList OceanDNA-b13482/target_genomes_gtdb.txt --output OceanDNA-b13482/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:38:26,227] [INFO] Task succeeded: fastANI
[2023-03-15 14:38:26,236] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:38:26,236] [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_002335055.1	s__Sulfurimonas sp002335055	98.6458	272	294	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	conclusive
GCA_003978465.1	s__Sulfurimonas sp003978465	88.6541	225	294	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	88.075	259	294	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	82.6694	167	294	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018698455.1	s__Sulfurimonas sp018698455	78.7289	140	294	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357825.1	s__Sulfurimonas sp017357825	78.6949	147	294	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	78.6532	157	294	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCA_002732645.1	s__Sulfurimonas sp002732645	78.2551	67	294	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	77.5794	113	294	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:38:26,236] [INFO] GTDB search result was written to OceanDNA-b13482/result_gtdb.tsv
[2023-03-15 14:38:26,236] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:38:26,238] [INFO] DFAST_QC result json was written to OceanDNA-b13482/dqc_result.json
[2023-03-15 14:38:26,238] [INFO] DFAST_QC completed!
[2023-03-15 14:38:26,238] [INFO] Total running time: 0h0m37s