[2023-03-15 04:38:20,729] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:38:20,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:38:20,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference
[2023-03-15 04:38:22,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:38:22,318] [INFO] Task started: Prodigal
[2023-03-15 04:38:22,318] [INFO] Running command: cat /var/lib/cwl/stg60aae6b3-3528-4763-80f9-f8f1deb2d1b8/OceanDNA-b7208.fa | prodigal -d OceanDNA-b7208/cds.fna -a OceanDNA-b7208/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:38:36,345] [INFO] Task succeeded: Prodigal
[2023-03-15 04:38:36,345] [INFO] Task started: HMMsearch
[2023-03-15 04:38:36,345] [INFO] Running command: hmmsearch --tblout OceanDNA-b7208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference/reference_markers.hmm OceanDNA-b7208/protein.faa > /dev/null
[2023-03-15 04:38:36,541] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:38:36,541] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg60aae6b3-3528-4763-80f9-f8f1deb2d1b8/OceanDNA-b7208.fa]
[2023-03-15 04:38:36,558] [INFO] Query marker FASTA was written to OceanDNA-b7208/markers.fasta
[2023-03-15 04:38:36,559] [INFO] Task started: Blastn
[2023-03-15 04:38:36,560] [INFO] Running command: blastn -query OceanDNA-b7208/markers.fasta -db /var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference/reference_markers.fasta -out OceanDNA-b7208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:38:37,106] [INFO] Task succeeded: Blastn
[2023-03-15 04:38:37,107] [INFO] Selected 18 target genomes.
[2023-03-15 04:38:37,107] [INFO] Target genome list was writen to OceanDNA-b7208/target_genomes.txt
[2023-03-15 04:38:37,122] [INFO] Task started: fastANI
[2023-03-15 04:38:37,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg60aae6b3-3528-4763-80f9-f8f1deb2d1b8/OceanDNA-b7208.fa --refList OceanDNA-b7208/target_genomes.txt --output OceanDNA-b7208/fastani_result.tsv --threads 1
[2023-03-15 04:38:49,253] [INFO] Task succeeded: fastANI
[2023-03-15 04:38:49,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:38:49,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:38:49,263] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:38:49,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 04:38:49,263] [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
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	85.1344	542	619	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	78.8378	265	619	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	78.6277	257	619	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	78.6135	256	619	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	78.3634	258	619	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	78.3307	179	619	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	78.2297	235	619	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	78.2039	226	619	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	77.717	187	619	95	below_threshold
Gramella fulva	strain=SH35	GCA_003024155.1	2126553	2126553	type	True	77.6836	143	619	95	below_threshold
Salegentibacter mishustinae	strain=DSM 23404	GCA_002900095.1	270918	270918	type	True	77.1901	121	619	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	77.1647	106	619	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	76.5148	113	619	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.4459	109	619	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 04:38:49,264] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7208/tc_result.tsv
[2023-03-15 04:38:49,264] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:38:49,264] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:38:49,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference/checkm_data
[2023-03-15 04:38:49,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:38:49,535] [INFO] Task started: CheckM
[2023-03-15 04:38:49,535] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7208/checkm_input OceanDNA-b7208/checkm_result
[2023-03-15 04:39:28,739] [INFO] Task succeeded: CheckM
[2023-03-15 04:39:28,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 04:39:28,985] [INFO] ===== Completeness check finished =====
[2023-03-15 04:39:28,985] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:39:28,985] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7208/markers.fasta)
[2023-03-15 04:39:28,987] [INFO] Task started: Blastn
[2023-03-15 04:39:28,987] [INFO] Running command: blastn -query OceanDNA-b7208/markers.fasta -db /var/lib/cwl/stg46047ffa-eea1-4de6-ac08-a63b0e4996c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:39:29,981] [INFO] Task succeeded: Blastn
[2023-03-15 04:39:29,982] [INFO] Selected 12 target genomes.
[2023-03-15 04:39:29,982] [INFO] Target genome list was writen to OceanDNA-b7208/target_genomes_gtdb.txt
[2023-03-15 04:39:29,991] [INFO] Task started: fastANI
[2023-03-15 04:39:29,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg60aae6b3-3528-4763-80f9-f8f1deb2d1b8/OceanDNA-b7208.fa --refList OceanDNA-b7208/target_genomes_gtdb.txt --output OceanDNA-b7208/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:39:37,532] [INFO] Task succeeded: fastANI
[2023-03-15 04:39:37,539] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:39:37,539] [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_006714895.1	s__Gramella sp006714895	92.2242	555	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423045.1	s__Gramella portivictoriae	85.154	541	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	78.8212	266	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_900105135.1	s__Gramella sp900105135	78.6905	247	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000060345.1	s__Gramella forsetii	78.6121	258	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003054225.1	s__Gramella gaetbulicola	78.3634	258	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889005.1	s__Gramella salexigens	78.3307	179	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050985.1	s__Gramella sabulilitoris	78.2039	226	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024155.1	s__Gramella fulva	77.7065	142	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001951155.1	s__Gramella flava	77.1969	168	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	99.04	98.07	0.94	0.88	3	-
GCF_002900095.1	s__Salegentibacter mishustinae	77.1901	121	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	4	-
GCF_900112105.1	s__Zunongwangia mangrovi	77.1419	107	619	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 04:39:37,539] [INFO] GTDB search result was written to OceanDNA-b7208/result_gtdb.tsv
[2023-03-15 04:39:37,539] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:39:37,541] [INFO] DFAST_QC result json was written to OceanDNA-b7208/dqc_result.json
[2023-03-15 04:39:37,541] [INFO] DFAST_QC completed!
[2023-03-15 04:39:37,541] [INFO] Total running time: 0h1m17s