[2023-03-16 06:33:31,989] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:33:31,989] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:33:31,990] [INFO] DQC Reference Directory: /var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference
[2023-03-16 06:33:33,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:33:33,083] [INFO] Task started: Prodigal
[2023-03-16 06:33:33,083] [INFO] Running command: cat /var/lib/cwl/stg6287e2bd-6b96-4f45-b401-357fe524ea02/OceanDNA-b17137.fa | prodigal -d OceanDNA-b17137/cds.fna -a OceanDNA-b17137/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:33:53,030] [INFO] Task succeeded: Prodigal
[2023-03-16 06:33:53,030] [INFO] Task started: HMMsearch
[2023-03-16 06:33:53,030] [INFO] Running command: hmmsearch --tblout OceanDNA-b17137/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference/reference_markers.hmm OceanDNA-b17137/protein.faa > /dev/null
[2023-03-16 06:33:53,231] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:33:53,232] [INFO] Found 6/6 markers.
[2023-03-16 06:33:53,250] [INFO] Query marker FASTA was written to OceanDNA-b17137/markers.fasta
[2023-03-16 06:33:53,251] [INFO] Task started: Blastn
[2023-03-16 06:33:53,251] [INFO] Running command: blastn -query OceanDNA-b17137/markers.fasta -db /var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference/reference_markers.fasta -out OceanDNA-b17137/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:33:53,855] [INFO] Task succeeded: Blastn
[2023-03-16 06:33:53,856] [INFO] Selected 13 target genomes.
[2023-03-16 06:33:53,856] [INFO] Target genome list was writen to OceanDNA-b17137/target_genomes.txt
[2023-03-16 06:33:53,865] [INFO] Task started: fastANI
[2023-03-16 06:33:53,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg6287e2bd-6b96-4f45-b401-357fe524ea02/OceanDNA-b17137.fa --refList OceanDNA-b17137/target_genomes.txt --output OceanDNA-b17137/fastani_result.tsv --threads 1
[2023-03-16 06:34:02,790] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:02,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:34:02,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:34:02,798] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 06:34:02,798] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 06:34:02,798] [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
Pseudodesulfovibrio profundus	strain=500-1	GCA_900217235.1	57320	57320	type	True	98.1334	972	1048	95	conclusive
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	78.6709	344	1048	95	below_threshold
Pseudodesulfovibrio piezophilus	strain=type strain: C1TLV30	GCA_000341895.1	879567	879567	type	True	78.4432	210	1048	95	below_threshold
Pseudodesulfovibrio indicus	strain=J2	GCA_001563225.1	1716143	1716143	type	True	78.3783	274	1048	95	below_threshold
Pseudodesulfovibrio indicus	strain=DSM 101483	GCA_004365595.1	1716143	1716143	type	True	78.2998	277	1048	95	below_threshold
Pseudodesulfovibrio sediminis	strain=SF6	GCA_020886695.1	2810563	2810563	type	True	78.235	283	1048	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	78.121	256	1048	95	below_threshold
Pseudodesulfovibrio alkaliphilus	strain=F-1	GCA_009729555.1	2661613	2661613	type	True	77.9149	196	1048	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	77.8849	252	1048	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	77.2476	171	1048	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:34:02,798] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17137/tc_result.tsv
[2023-03-16 06:34:02,798] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:34:02,798] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:34:02,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference/checkm_data
[2023-03-16 06:34:02,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:34:02,804] [INFO] Task started: CheckM
[2023-03-16 06:34:02,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17137/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17137/checkm_input OceanDNA-b17137/checkm_result
[2023-03-16 06:34:53,982] [INFO] Task succeeded: CheckM
[2023-03-16 06:34:53,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:34:53,985] [INFO] ===== Completeness check finished =====
[2023-03-16 06:34:53,985] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:34:53,985] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17137/markers.fasta)
[2023-03-16 06:34:53,985] [INFO] Task started: Blastn
[2023-03-16 06:34:53,985] [INFO] Running command: blastn -query OceanDNA-b17137/markers.fasta -db /var/lib/cwl/stg98410016-f77b-4b97-8bd6-9a849d216526/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17137/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:34:55,011] [INFO] Task succeeded: Blastn
[2023-03-16 06:34:55,011] [INFO] Selected 13 target genomes.
[2023-03-16 06:34:55,012] [INFO] Target genome list was writen to OceanDNA-b17137/target_genomes_gtdb.txt
[2023-03-16 06:34:55,024] [INFO] Task started: fastANI
[2023-03-16 06:34:55,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg6287e2bd-6b96-4f45-b401-357fe524ea02/OceanDNA-b17137.fa --refList OceanDNA-b17137/target_genomes_gtdb.txt --output OceanDNA-b17137/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:35:03,269] [INFO] Task succeeded: fastANI
[2023-03-16 06:35:03,277] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:35:03,277] [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_900217235.1	s__Pseudodesulfovibrio profundus	98.1334	972	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	98.02	97.98	0.88	0.83	5	conclusive
GCF_012516435.1	s__Pseudodesulfovibrio sp012516435	79.1912	359	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762795.1	s__Pseudodesulfovibrio cashew	78.6709	344	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744135.1	s__Pseudodesulfovibrio sp016744135	78.4637	198	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341895.1	s__Pseudodesulfovibrio piezophilus	78.4448	210	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563225.1	s__Pseudodesulfovibrio indicus	78.3783	274	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001874525.1	s__Pseudodesulfovibrio hydrargyri	78.121	256	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468615.1	s__Pseudodesulfovibrio sp010468615	78.0869	193	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729555.1	s__Pseudodesulfovibrio sp009729555	77.9149	196	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017351175.1	s__Pseudodesulfovibrio sp017351175	77.898	238	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176915.2	s__Pseudodesulfovibrio aespoeensis	77.8849	252	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.98	99.94	1.00	0.98	8	-
GCA_015709315.1	s__Pseudodesulfovibrio sp015709315	77.8831	251	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008830225.1	s__Pseudodesulfovibrio senegalensis	77.2373	152	1048	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:35:03,277] [INFO] GTDB search result was written to OceanDNA-b17137/result_gtdb.tsv
[2023-03-16 06:35:03,277] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:35:03,279] [INFO] DFAST_QC result json was written to OceanDNA-b17137/dqc_result.json
[2023-03-16 06:35:03,279] [INFO] DFAST_QC completed!
[2023-03-16 06:35:03,279] [INFO] Total running time: 0h1m31s