[2023-03-16 02:38:05,013] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:05,013] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:05,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference
[2023-03-16 02:38:06,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,293] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,293] [INFO] Running command: cat /var/lib/cwl/stg2ca1add3-e92d-41ba-b607-82170c0291c0/OceanDNA-b35100.fa | prodigal -d OceanDNA-b35100/cds.fna -a OceanDNA-b35100/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:27,258] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:27,258] [INFO] Task started: HMMsearch
[2023-03-16 02:38:27,258] [INFO] Running command: hmmsearch --tblout OceanDNA-b35100/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference/reference_markers.hmm OceanDNA-b35100/protein.faa > /dev/null
[2023-03-16 02:38:27,533] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:27,533] [INFO] Found 6/6 markers.
[2023-03-16 02:38:27,559] [INFO] Query marker FASTA was written to OceanDNA-b35100/markers.fasta
[2023-03-16 02:38:27,559] [INFO] Task started: Blastn
[2023-03-16 02:38:27,559] [INFO] Running command: blastn -query OceanDNA-b35100/markers.fasta -db /var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference/reference_markers.fasta -out OceanDNA-b35100/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:28,233] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:28,234] [INFO] Selected 16 target genomes.
[2023-03-16 02:38:28,234] [INFO] Target genome list was writen to OceanDNA-b35100/target_genomes.txt
[2023-03-16 02:38:28,284] [INFO] Task started: fastANI
[2023-03-16 02:38:28,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca1add3-e92d-41ba-b607-82170c0291c0/OceanDNA-b35100.fa --refList OceanDNA-b35100/target_genomes.txt --output OceanDNA-b35100/fastani_result.tsv --threads 1
[2023-03-16 02:38:41,670] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:41,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:41,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:41,680] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2023-03-16 02:38:41,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 02:38:41,680] [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
Pseudoalteromonas tunicata	strain=D2	GCA_003568825.1	314281	314281	type	True	98.9826	1226	1272	95	conclusive
Pseudoalteromonas tunicata	strain=D2	GCA_000153245.1	314281	314281	type	True	98.9794	1229	1272	95	conclusive
Pseudoalteromonas tunicata	strain=D2	GCA_002310815.1	314281	314281	type	True	98.9776	1224	1272	95	conclusive
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	79.6945	537	1272	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	77.9313	183	1272	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	77.8071	202	1272	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	77.7862	204	1272	95	below_threshold
Pseudoalteromonas undina	strain=DSM 6065	GCA_000238275.4	43660	43660	type	True	77.7598	209	1272	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.6398	219	1272	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	77.6294	220	1272	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	77.5624	214	1272	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	76.4349	62	1272	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	75.9599	80	1272	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 02:38:41,680] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35100/tc_result.tsv
[2023-03-16 02:38:41,680] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:41,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:41,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference/checkm_data
[2023-03-16 02:38:41,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:41,688] [INFO] Task started: CheckM
[2023-03-16 02:38:41,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35100/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35100/checkm_input OceanDNA-b35100/checkm_result
[2023-03-16 02:39:33,953] [INFO] Task succeeded: CheckM
[2023-03-16 02:39:33,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 02:39:33,980] [INFO] ===== Completeness check finished =====
[2023-03-16 02:39:33,981] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:39:33,981] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35100/markers.fasta)
[2023-03-16 02:39:33,981] [INFO] Task started: Blastn
[2023-03-16 02:39:33,981] [INFO] Running command: blastn -query OceanDNA-b35100/markers.fasta -db /var/lib/cwl/stg374f4ee3-c2cd-4db3-bd24-7a66b108750c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35100/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:39:35,033] [INFO] Task succeeded: Blastn
[2023-03-16 02:39:35,034] [INFO] Selected 24 target genomes.
[2023-03-16 02:39:35,034] [INFO] Target genome list was writen to OceanDNA-b35100/target_genomes_gtdb.txt
[2023-03-16 02:39:35,164] [INFO] Task started: fastANI
[2023-03-16 02:39:35,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca1add3-e92d-41ba-b607-82170c0291c0/OceanDNA-b35100.fa --refList OceanDNA-b35100/target_genomes_gtdb.txt --output OceanDNA-b35100/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:53,461] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:53,475] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:53,475] [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_002310815.1	s__Pseudoalteromonas tunicata	98.9776	1224	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_014925405.1	s__Pseudoalteromonas ulvae	79.689	537	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.81	98.81	0.93	0.93	2	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	77.9677	193	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	77.9462	193	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	77.9266	233	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
GCF_000238355.1	s__Pseudoalteromonas haloplanktis	77.922	219	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.55	99.12	0.96	0.93	3	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	77.8477	207	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_000238395.3	s__Pseudoalteromonas arctica	77.7547	206	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCA_018402495.1	s__Pseudoalteromonas sp018402495	77.75	211	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.7416	203	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_004328665.1	s__Pseudoalteromonas sp001974855	77.74	215	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.16	95.35	0.86	0.83	5	-
GCF_000238275.3	s__Pseudoalteromonas undina	77.7298	211	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	96.09	0.91	0.86	14	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	77.7036	203	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
GCF_001469215.1	s__Pseudoalteromonas sp001469215	77.6785	217	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165575.1	s__Pseudoalteromonas sp002165575	77.6761	212	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100985.1	s__Pseudoalteromonas sp018100985	77.6733	200	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.38	98.38	0.93	0.93	2	-
GCF_900239935.1	s__Pseudoalteromonas carrageenovora	77.6621	213	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.00	96.44	0.97	0.91	6	-
GCF_900116435.1	s__Pseudoalteromonas lipolytica	77.6591	202	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.6439	218	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_002310835.1	s__Pseudoalteromonas tetraodonis	77.6438	219	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	96.28	0.91	0.84	28	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	77.593	215	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_001465295.1	s__Pseudoalteromonas translucida	77.5624	214	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.0242	N/A	N/A	N/A	N/A	1	-
GCF_000238335.3	s__Pseudoalteromonas marina	77.3814	185	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.76	97.57	0.91	0.88	12	-
GCF_000788395.1	s__Pseudoalteromonas piratica	77.3168	191	1272	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:53,475] [INFO] GTDB search result was written to OceanDNA-b35100/result_gtdb.tsv
[2023-03-16 02:39:53,475] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:53,478] [INFO] DFAST_QC result json was written to OceanDNA-b35100/dqc_result.json
[2023-03-16 02:39:53,478] [INFO] DFAST_QC completed!
[2023-03-16 02:39:53,478] [INFO] Total running time: 0h1m48s