[2023-03-19 05:19:33,814] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,814] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,814] [INFO] DQC Reference Directory: /var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference
[2023-03-19 05:19:35,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,401] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,402] [INFO] Running command: cat /var/lib/cwl/stg79d82d9a-2e52-47dd-adbb-311264099143/OceanDNA-b9706.fa | prodigal -d OceanDNA-b9706/cds.fna -a OceanDNA-b9706/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:50,637] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:50,637] [INFO] Task started: HMMsearch
[2023-03-19 05:19:50,637] [INFO] Running command: hmmsearch --tblout OceanDNA-b9706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference/reference_markers.hmm OceanDNA-b9706/protein.faa > /dev/null
[2023-03-19 05:19:50,833] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:50,833] [INFO] Found 6/6 markers.
[2023-03-19 05:19:50,851] [INFO] Query marker FASTA was written to OceanDNA-b9706/markers.fasta
[2023-03-19 05:19:50,851] [INFO] Task started: Blastn
[2023-03-19 05:19:50,851] [INFO] Running command: blastn -query OceanDNA-b9706/markers.fasta -db /var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference/reference_markers.fasta -out OceanDNA-b9706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:51,443] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:51,444] [INFO] Selected 21 target genomes.
[2023-03-19 05:19:51,444] [INFO] Target genome list was writen to OceanDNA-b9706/target_genomes.txt
[2023-03-19 05:19:51,456] [INFO] Task started: fastANI
[2023-03-19 05:19:51,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg79d82d9a-2e52-47dd-adbb-311264099143/OceanDNA-b9706.fa --refList OceanDNA-b9706/target_genomes.txt --output OceanDNA-b9706/fastani_result.tsv --threads 1
[2023-03-19 05:20:04,244] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:04,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:04,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:04,256] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:04,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:20:04,256] [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
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	89.4873	615	756	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	80.5857	432	756	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.6522	114	756	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	77.696	157	756	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	77.6754	156	756	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.4474	95	756	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	77.3242	156	756	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	77.2551	125	756	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.0101	57	756	95	below_threshold
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	77.0023	67	756	95	below_threshold
Patiriisocius marinus	strain=NBRC 109484	GCA_008974325.1	1397112	1397112	type	True	76.9804	128	756	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.8974	128	756	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.7637	61	756	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	76.7095	69	756	95	below_threshold
Winogradskyella wandonensis	strain=CECT 8445	GCA_004346845.1	1442586	1442586	type	True	76.6466	51	756	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5872	78	756	95	below_threshold
Mangrovimonas spongiae	strain=HN-E26	GCA_003944795.1	2494697	2494697	type	True	76.5208	67	756	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	76.4356	72	756	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.3792	72	756	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.3068	65	756	95	below_threshold
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	76.1685	69	756	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:20:04,257] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9706/tc_result.tsv
[2023-03-19 05:20:04,257] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:04,257] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:04,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference/checkm_data
[2023-03-19 05:20:04,258] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:04,261] [INFO] Task started: CheckM
[2023-03-19 05:20:04,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9706/checkm_input OceanDNA-b9706/checkm_result
[2023-03-19 05:20:44,501] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:44,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:44,503] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:44,503] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:44,503] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9706/markers.fasta)
[2023-03-19 05:20:44,504] [INFO] Task started: Blastn
[2023-03-19 05:20:44,504] [INFO] Running command: blastn -query OceanDNA-b9706/markers.fasta -db /var/lib/cwl/stg62903929-8572-4811-85a3-add4335196e4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:45,347] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:45,347] [INFO] Selected 8 target genomes.
[2023-03-19 05:20:45,348] [INFO] Target genome list was writen to OceanDNA-b9706/target_genomes_gtdb.txt
[2023-03-19 05:20:45,355] [INFO] Task started: fastANI
[2023-03-19 05:20:45,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg79d82d9a-2e52-47dd-adbb-311264099143/OceanDNA-b9706.fa --refList OceanDNA-b9706/target_genomes_gtdb.txt --output OceanDNA-b9706/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:49,923] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:49,929] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 05:20:49,929] [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_003413745.1	s__Marixanthomonas ophiurae	89.4873	615	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364245.1	s__Marixanthomonas sp002364245	88.0139	377	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002631855.1	s__Marixanthomonas sp002631855	87.7754	576	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002360635.1	s__Marixanthomonas sp002360635	86.5091	554	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	98.57	97.61	0.95	0.92	4	-
GCF_003095375.1	s__Marixanthomonas sp003095375	80.5857	432	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337605.1	s__Marinirhabdus sp002337605	77.7714	140	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	77.3242	156	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944795.1	s__Mangrovimonas spongiae	76.5208	67	756	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:49,929] [INFO] GTDB search result was written to OceanDNA-b9706/result_gtdb.tsv
[2023-03-19 05:20:49,929] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:49,931] [INFO] DFAST_QC result json was written to OceanDNA-b9706/dqc_result.json
[2023-03-19 05:20:49,931] [INFO] DFAST_QC completed!
[2023-03-19 05:20:49,931] [INFO] Total running time: 0h1m16s