[2023-03-15 17:28:53,482] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:28:53,482] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:28:53,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference
[2023-03-15 17:28:54,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:28:54,586] [INFO] Task started: Prodigal
[2023-03-15 17:28:54,586] [INFO] Running command: cat /var/lib/cwl/stgdb26d84a-73a4-4c12-8b64-e891106567d7/OceanDNA-b34640.fa | prodigal -d OceanDNA-b34640/cds.fna -a OceanDNA-b34640/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:29:23,170] [INFO] Task succeeded: Prodigal
[2023-03-15 17:29:23,170] [INFO] Task started: HMMsearch
[2023-03-15 17:29:23,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b34640/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference/reference_markers.hmm OceanDNA-b34640/protein.faa > /dev/null
[2023-03-15 17:29:23,426] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:29:23,427] [INFO] Found 6/6 markers.
[2023-03-15 17:29:23,462] [INFO] Query marker FASTA was written to OceanDNA-b34640/markers.fasta
[2023-03-15 17:29:23,463] [INFO] Task started: Blastn
[2023-03-15 17:29:23,463] [INFO] Running command: blastn -query OceanDNA-b34640/markers.fasta -db /var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference/reference_markers.fasta -out OceanDNA-b34640/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:29:24,090] [INFO] Task succeeded: Blastn
[2023-03-15 17:29:24,091] [INFO] Selected 24 target genomes.
[2023-03-15 17:29:24,092] [INFO] Target genome list was writen to OceanDNA-b34640/target_genomes.txt
[2023-03-15 17:29:24,167] [INFO] Task started: fastANI
[2023-03-15 17:29:24,167] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb26d84a-73a4-4c12-8b64-e891106567d7/OceanDNA-b34640.fa --refList OceanDNA-b34640/target_genomes.txt --output OceanDNA-b34640/fastani_result.tsv --threads 1
[2023-03-15 17:29:41,147] [INFO] Task succeeded: fastANI
[2023-03-15 17:29:41,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:29:41,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:29:41,159] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:29:41,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:29:41,159] [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
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.4219	361	1836	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.1792	308	1836	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.0808	305	1836	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9272	236	1836	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.8145	229	1836	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	77.6673	289	1836	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.499	263	1836	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.4156	216	1836	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.3759	235	1836	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.3315	235	1836	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.0876	215	1836	95	below_threshold
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	76.9782	112	1836	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	76.9429	187	1836	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	76.5941	146	1836	95	below_threshold
Thalassotalea mangrovi	strain=ZS-4	GCA_005116735.1	2572245	2572245	type	True	76.4492	59	1836	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	75.9097	56	1836	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	75.9092	56	1836	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	75.7151	54	1836	95	below_threshold
Shewanella surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	75.2825	54	1836	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	74.9492	50	1836	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:29:41,160] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34640/tc_result.tsv
[2023-03-15 17:29:41,161] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:29:41,161] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:29:41,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference/checkm_data
[2023-03-15 17:29:41,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:29:41,238] [INFO] Task started: CheckM
[2023-03-15 17:29:41,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34640/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34640/checkm_input OceanDNA-b34640/checkm_result
[2023-03-15 17:30:50,392] [INFO] Task succeeded: CheckM
[2023-03-15 17:30:50,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:30:50,419] [INFO] ===== Completeness check finished =====
[2023-03-15 17:30:50,419] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:30:50,419] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34640/markers.fasta)
[2023-03-15 17:30:50,420] [INFO] Task started: Blastn
[2023-03-15 17:30:50,420] [INFO] Running command: blastn -query OceanDNA-b34640/markers.fasta -db /var/lib/cwl/stg196088b0-6f89-4c69-83cb-5e017624ff17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34640/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:30:51,415] [INFO] Task succeeded: Blastn
[2023-03-15 17:30:51,416] [INFO] Selected 30 target genomes.
[2023-03-15 17:30:51,416] [INFO] Target genome list was writen to OceanDNA-b34640/target_genomes_gtdb.txt
[2023-03-15 17:30:51,537] [INFO] Task started: fastANI
[2023-03-15 17:30:51,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb26d84a-73a4-4c12-8b64-e891106567d7/OceanDNA-b34640.fa --refList OceanDNA-b34640/target_genomes_gtdb.txt --output OceanDNA-b34640/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:31:16,193] [INFO] Task succeeded: fastANI
[2023-03-15 17:31:16,209] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:31:16,209] [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_013215655.1	s__Colwellia_A sp013215655	78.5842	362	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215385.1	s__Colwellia_A sp013215385	78.5498	332	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378625.1	s__Colwellia piezophila	78.4593	359	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.3922	346	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001440345.1	s__Colwellia sp001440345	78.3122	308	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	78.2463	362	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_007954275.1	s__Colwellia demingiae	78.1671	309	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216005.1	s__JABSOI01 sp013216005	78.135	243	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	78.0989	268	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002207865.1	s__Colwellia marinimaniae	78.0777	306	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCA_013215465.1	s__Colwellia sp013215465	77.9574	308	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCA_002733765.1	s__Colwellia sp002733765	77.8783	288	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.7459	270	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	77.7362	266	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013216015.1	s__JABSOI01 sp013216015	77.7293	293	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__JABSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	77.7292	362	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	77.7191	256	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954355.1	s__Colwellia_A hornerae	77.6825	287	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	77.5821	256	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	77.5541	264	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001767295.1	s__Colwellia_A sp001767295	77.5201	287	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	96.63	96.27	0.86	0.85	17	-
GCF_002076895.1	s__Cognaticolwellia beringensis	77.4398	237	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	77.3876	247	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.1393	179	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653195.1	s__Thalassotalea_B profundi	77.0994	214	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	76.9566	186	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	76.6883	59	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005843925.1	s__Thalassotalea_A litorea	76.6058	76	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	76.5941	146	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	76.592	175	1836	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:31:16,210] [INFO] GTDB search result was written to OceanDNA-b34640/result_gtdb.tsv
[2023-03-15 17:31:16,210] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:31:16,213] [INFO] DFAST_QC result json was written to OceanDNA-b34640/dqc_result.json
[2023-03-15 17:31:16,213] [INFO] DFAST_QC completed!
[2023-03-15 17:31:16,213] [INFO] Total running time: 0h2m23s