[2023-03-18 01:41:22,928] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:41:22,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:41:22,928] [INFO] DQC Reference Directory: /var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference
[2023-03-18 01:41:24,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:41:24,099] [INFO] Task started: Prodigal
[2023-03-18 01:41:24,099] [INFO] Running command: cat /var/lib/cwl/stg9e46c9be-d6cb-43ca-af49-6e7dde2425d0/OceanDNA-b24254.fa | prodigal -d OceanDNA-b24254/cds.fna -a OceanDNA-b24254/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:41:37,911] [INFO] Task succeeded: Prodigal
[2023-03-18 01:41:37,911] [INFO] Task started: HMMsearch
[2023-03-18 01:41:37,911] [INFO] Running command: hmmsearch --tblout OceanDNA-b24254/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference/reference_markers.hmm OceanDNA-b24254/protein.faa > /dev/null
[2023-03-18 01:41:38,093] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:41:38,093] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9e46c9be-d6cb-43ca-af49-6e7dde2425d0/OceanDNA-b24254.fa]
[2023-03-18 01:41:38,117] [INFO] Query marker FASTA was written to OceanDNA-b24254/markers.fasta
[2023-03-18 01:41:38,117] [INFO] Task started: Blastn
[2023-03-18 01:41:38,117] [INFO] Running command: blastn -query OceanDNA-b24254/markers.fasta -db /var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference/reference_markers.fasta -out OceanDNA-b24254/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:41:38,664] [INFO] Task succeeded: Blastn
[2023-03-18 01:41:38,665] [INFO] Selected 19 target genomes.
[2023-03-18 01:41:38,665] [INFO] Target genome list was writen to OceanDNA-b24254/target_genomes.txt
[2023-03-18 01:41:38,679] [INFO] Task started: fastANI
[2023-03-18 01:41:38,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e46c9be-d6cb-43ca-af49-6e7dde2425d0/OceanDNA-b24254.fa --refList OceanDNA-b24254/target_genomes.txt --output OceanDNA-b24254/fastani_result.tsv --threads 1
[2023-03-18 01:41:52,539] [INFO] Task succeeded: fastANI
[2023-03-18 01:41:52,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:41:52,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:41:52,551] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:41:52,551] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:41:52,551] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.122	84	669	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.9762	87	669	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.9546	171	669	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.9279	86	669	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	75.8816	114	669	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	75.7071	73	669	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.6547	117	669	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.6471	118	669	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.6421	68	669	95	below_threshold
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	75.6183	67	669	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.5335	104	669	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.5264	76	669	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.4028	126	669	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.4028	126	669	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	75.3913	104	669	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_004362995.1	1264899	1264899	type	True	75.3845	105	669	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.2203	88	669	95	below_threshold
Brevundimonas diminuta	strain=ATCC 11568	GCA_000204035.1	293	293	type	True	75.0762	55	669	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:41:52,551] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24254/tc_result.tsv
[2023-03-18 01:41:52,551] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:41:52,551] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:41:52,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference/checkm_data
[2023-03-18 01:41:52,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:41:52,557] [INFO] Task started: CheckM
[2023-03-18 01:41:52,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24254/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24254/checkm_input OceanDNA-b24254/checkm_result
[2023-03-18 01:42:29,868] [INFO] Task succeeded: CheckM
[2023-03-18 01:42:29,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.86%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:42:29,871] [INFO] ===== Completeness check finished =====
[2023-03-18 01:42:29,871] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:42:29,872] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24254/markers.fasta)
[2023-03-18 01:42:29,875] [INFO] Task started: Blastn
[2023-03-18 01:42:29,875] [INFO] Running command: blastn -query OceanDNA-b24254/markers.fasta -db /var/lib/cwl/stga3a5c49d-c1a2-40f3-bf7b-4911505c070e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24254/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:42:30,596] [INFO] Task succeeded: Blastn
[2023-03-18 01:42:30,597] [INFO] Selected 16 target genomes.
[2023-03-18 01:42:30,597] [INFO] Target genome list was writen to OceanDNA-b24254/target_genomes_gtdb.txt
[2023-03-18 01:42:30,609] [INFO] Task started: fastANI
[2023-03-18 01:42:30,609] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e46c9be-d6cb-43ca-af49-6e7dde2425d0/OceanDNA-b24254.fa --refList OceanDNA-b24254/target_genomes_gtdb.txt --output OceanDNA-b24254/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:42:42,592] [INFO] Task succeeded: fastANI
[2023-03-18 01:42:42,601] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:42:42,602] [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_018701215.1	s__GCA-2731375 sp018701215	77.2356	219	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.97	99.95	0.98	0.97	15	-
GCA_002731375.1	s__GCA-2731375 sp002731375	76.9306	167	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.58	99.58	0.91	0.91	2	-
GCA_018667855.1	s__GCA-2731375 sp018667855	76.9012	203	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	99.62	99.58	0.85	0.84	3	-
GCA_016776605.1	s__GCA-2731375 sp016776605	76.8398	210	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__GCA-2731375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869175.1	s__VGEV01 sp016869175	76.2879	126	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__VGEV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.1246	144	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	75.9141	174	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796975.1	s__Ferrovibrio sp002796975	75.7497	71	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	75.7071	73	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCF_011022235.1	s__Magnetospirillum aberrantis	75.6296	69	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197755.1	s__Ferrovibrio terrae	75.6183	67	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898825.1	s__Magnetospirillum sp001898825	75.5973	75	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	95.98	95.98	0.88	0.88	2	-
GCA_903901915.1	s__Phaeospirillum sp903901915	75.5945	80	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.99	99.99	0.95	0.95	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	75.5728	146	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218045.1	s__Magnetospirillum sp006218045	75.4287	77	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCA_016195085.1	s__JACQAG01 sp016195085	75.4269	68	669	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:42:42,602] [INFO] GTDB search result was written to OceanDNA-b24254/result_gtdb.tsv
[2023-03-18 01:42:42,602] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:42:42,604] [INFO] DFAST_QC result json was written to OceanDNA-b24254/dqc_result.json
[2023-03-18 01:42:42,604] [INFO] DFAST_QC completed!
[2023-03-18 01:42:42,604] [INFO] Total running time: 0h1m20s