[2023-03-16 04:05:20,416] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:05:20,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:05:20,417] [INFO] DQC Reference Directory: /var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference
[2023-03-16 04:05:22,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:05:22,128] [INFO] Task started: Prodigal
[2023-03-16 04:05:22,128] [INFO] Running command: cat /var/lib/cwl/stg474db5a9-7834-40a0-8435-9e41226d3214/OceanDNA-b7476.fa | prodigal -d OceanDNA-b7476/cds.fna -a OceanDNA-b7476/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:05:44,762] [INFO] Task succeeded: Prodigal
[2023-03-16 04:05:44,763] [INFO] Task started: HMMsearch
[2023-03-16 04:05:44,763] [INFO] Running command: hmmsearch --tblout OceanDNA-b7476/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference/reference_markers.hmm OceanDNA-b7476/protein.faa > /dev/null
[2023-03-16 04:05:44,979] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:05:44,980] [INFO] Found 6/6 markers.
[2023-03-16 04:05:45,004] [INFO] Query marker FASTA was written to OceanDNA-b7476/markers.fasta
[2023-03-16 04:05:45,004] [INFO] Task started: Blastn
[2023-03-16 04:05:45,004] [INFO] Running command: blastn -query OceanDNA-b7476/markers.fasta -db /var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference/reference_markers.fasta -out OceanDNA-b7476/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:05:45,574] [INFO] Task succeeded: Blastn
[2023-03-16 04:05:45,575] [INFO] Selected 28 target genomes.
[2023-03-16 04:05:45,575] [INFO] Target genome list was writen to OceanDNA-b7476/target_genomes.txt
[2023-03-16 04:05:45,588] [INFO] Task started: fastANI
[2023-03-16 04:05:45,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg474db5a9-7834-40a0-8435-9e41226d3214/OceanDNA-b7476.fa --refList OceanDNA-b7476/target_genomes.txt --output OceanDNA-b7476/fastani_result.tsv --threads 1
[2023-03-16 04:06:02,515] [INFO] Task succeeded: fastANI
[2023-03-16 04:06:02,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:06:02,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:06:02,528] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:06:02,528] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:06:02,528] [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
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	76.8346	175	1156	95	below_threshold
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	76.795	172	1156	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	76.7801	168	1156	95	below_threshold
Leeuwenhoekiella nanhaiensis	strain=G18	GCA_002744755.1	1655491	1655491	type	True	76.6398	123	1156	95	below_threshold
Leeuwenhoekiella aequorea	strain=LMG 22550	GCA_004104375.1	283736	283736	type	True	76.6233	168	1156	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	76.5612	159	1156	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	76.5506	165	1156	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	76.5399	157	1156	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.1524	54	1156	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	75.9857	54	1156	95	below_threshold
Dokdonia pacifica	strain=DSM 25597	GCA_900188275.1	1627892	1627892	type	True	75.9426	72	1156	95	below_threshold
Dokdonia pacifica	strain=CGMCC 1.12184	GCA_014636685.1	1627892	1627892	type	True	75.9162	73	1156	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	75.8788	57	1156	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	75.7797	54	1156	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	75.7718	55	1156	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	75.7718	55	1156	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	75.7701	57	1156	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	75.767	57	1156	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	75.7263	73	1156	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	75.6862	61	1156	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	75.303	54	1156	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	75.1914	54	1156	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:06:02,550] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7476/tc_result.tsv
[2023-03-16 04:06:02,550] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:06:02,550] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:06:02,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference/checkm_data
[2023-03-16 04:06:02,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:06:02,569] [INFO] Task started: CheckM
[2023-03-16 04:06:02,569] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7476/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7476/checkm_input OceanDNA-b7476/checkm_result
[2023-03-16 04:06:59,347] [INFO] Task succeeded: CheckM
[2023-03-16 04:06:59,348] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:06:59,350] [INFO] ===== Completeness check finished =====
[2023-03-16 04:06:59,351] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:06:59,351] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7476/markers.fasta)
[2023-03-16 04:06:59,351] [INFO] Task started: Blastn
[2023-03-16 04:06:59,351] [INFO] Running command: blastn -query OceanDNA-b7476/markers.fasta -db /var/lib/cwl/stge4bd71ad-e861-46be-be79-6c751d67008f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7476/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:07:00,154] [INFO] Task succeeded: Blastn
[2023-03-16 04:07:00,155] [INFO] Selected 25 target genomes.
[2023-03-16 04:07:00,155] [INFO] Target genome list was writen to OceanDNA-b7476/target_genomes_gtdb.txt
[2023-03-16 04:07:00,174] [INFO] Task started: fastANI
[2023-03-16 04:07:00,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg474db5a9-7834-40a0-8435-9e41226d3214/OceanDNA-b7476.fa --refList OceanDNA-b7476/target_genomes_gtdb.txt --output OceanDNA-b7476/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:07:16,375] [INFO] Task succeeded: fastANI
[2023-03-16 04:07:16,387] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:07:16,387] [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_000687915.1	s__Leeuwenhoekiella sp000687915	77.1809	183	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129005.1	s__Leeuwenhoekiella marinoflava	76.795	172	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	76.7801	168	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_004104375.1	s__Leeuwenhoekiella aequorea	76.6233	168	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	76.5612	159	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	76.5506	165	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_004104075.1	s__Leeuwenhoekiella polynyae	76.5372	173	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050015.1	s__Leeuwenhoekiella sp011050015	76.2257	89	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	75.9857	54	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012931685.1	s__Pseudobizionia ponticola	75.8788	57	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_000211855.2	s__Lacinutrix sp000211855	75.8351	74	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	75.7796	60	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_900141715.1	s__Arenitalea lutea	75.7718	55	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900299535.1	s__Aquimarina sp900299535	75.7343	75	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_900109375.1	s__Aquimarina amphilecti	75.7263	73	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000212355.1	s__Dokdonia sp000212355	75.7174	74	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	98.49	98.49	0.97	0.97	2	-
GCF_001685485.1	s__Formosa haliotis	75.7012	63	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Formosa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095655.1	s__Dokdonia sp003095655	75.6999	85	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Dokdonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	75.663	78	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_900109345.1	s__Maribacter orientalis	75.303	54	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	75.1914	54	1156	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 04:07:16,387] [INFO] GTDB search result was written to OceanDNA-b7476/result_gtdb.tsv
[2023-03-16 04:07:16,387] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:07:16,389] [INFO] DFAST_QC result json was written to OceanDNA-b7476/dqc_result.json
[2023-03-16 04:07:16,390] [INFO] DFAST_QC completed!
[2023-03-16 04:07:16,390] [INFO] Total running time: 0h1m56s