[2023-03-15 08:14:06,392] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:14:06,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:14:06,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference
[2023-03-15 08:14:07,507] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:14:07,507] [INFO] Task started: Prodigal
[2023-03-15 08:14:07,507] [INFO] Running command: cat /var/lib/cwl/stgf7ac0965-979e-43b2-a80b-a7782fcb176b/OceanDNA-b1781.fa | prodigal -d OceanDNA-b1781/cds.fna -a OceanDNA-b1781/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:14:21,123] [INFO] Task succeeded: Prodigal
[2023-03-15 08:14:21,123] [INFO] Task started: HMMsearch
[2023-03-15 08:14:21,124] [INFO] Running command: hmmsearch --tblout OceanDNA-b1781/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference/reference_markers.hmm OceanDNA-b1781/protein.faa > /dev/null
[2023-03-15 08:14:21,303] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:14:21,304] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf7ac0965-979e-43b2-a80b-a7782fcb176b/OceanDNA-b1781.fa]
[2023-03-15 08:14:21,328] [INFO] Query marker FASTA was written to OceanDNA-b1781/markers.fasta
[2023-03-15 08:14:21,330] [INFO] Task started: Blastn
[2023-03-15 08:14:21,330] [INFO] Running command: blastn -query OceanDNA-b1781/markers.fasta -db /var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference/reference_markers.fasta -out OceanDNA-b1781/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:14:21,961] [INFO] Task succeeded: Blastn
[2023-03-15 08:14:21,963] [INFO] Selected 23 target genomes.
[2023-03-15 08:14:21,963] [INFO] Target genome list was writen to OceanDNA-b1781/target_genomes.txt
[2023-03-15 08:14:21,975] [INFO] Task started: fastANI
[2023-03-15 08:14:21,975] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7ac0965-979e-43b2-a80b-a7782fcb176b/OceanDNA-b1781.fa --refList OceanDNA-b1781/target_genomes.txt --output OceanDNA-b1781/fastani_result.tsv --threads 1
[2023-03-15 08:14:40,205] [INFO] Task succeeded: fastANI
[2023-03-15 08:14:40,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:14:40,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:14:40,216] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:14:40,216] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:14:40,217] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.2591	102	641	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.1463	62	641	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.0383	117	641	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.7905	113	641	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.7098	88	641	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.5871	107	641	95	below_threshold
Gordonia paraffinivorans	strain=NBRC 108238	GCA_000344155.1	175628	175628	type	True	75.2796	60	641	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	75.0807	69	641	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	75.0069	84	641	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	75.0066	84	641	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	75.0027	76	641	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	75.0008	82	641	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	74.9898	93	641	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	74.9752	78	641	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	74.9447	79	641	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	74.8597	68	641	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	74.815	58	641	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	74.7938	61	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:14:40,217] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1781/tc_result.tsv
[2023-03-15 08:14:40,217] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:14:40,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:14:40,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference/checkm_data
[2023-03-15 08:14:40,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:14:40,258] [INFO] Task started: CheckM
[2023-03-15 08:14:40,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1781/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1781/checkm_input OceanDNA-b1781/checkm_result
[2023-03-15 08:15:27,908] [INFO] Task succeeded: CheckM
[2023-03-15 08:15:27,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.97%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:15:27,915] [INFO] ===== Completeness check finished =====
[2023-03-15 08:15:27,916] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:15:27,916] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1781/markers.fasta)
[2023-03-15 08:15:27,917] [INFO] Task started: Blastn
[2023-03-15 08:15:27,917] [INFO] Running command: blastn -query OceanDNA-b1781/markers.fasta -db /var/lib/cwl/stgcfbe85c2-db0c-4704-b27e-f77bf1be1771/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1781/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:15:28,911] [INFO] Task succeeded: Blastn
[2023-03-15 08:15:28,914] [INFO] Selected 13 target genomes.
[2023-03-15 08:15:28,914] [INFO] Target genome list was writen to OceanDNA-b1781/target_genomes_gtdb.txt
[2023-03-15 08:15:28,923] [INFO] Task started: fastANI
[2023-03-15 08:15:28,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7ac0965-979e-43b2-a80b-a7782fcb176b/OceanDNA-b1781.fa --refList OceanDNA-b1781/target_genomes_gtdb.txt --output OceanDNA-b1781/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:15:35,513] [INFO] Task succeeded: fastANI
[2023-03-15 08:15:35,519] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:15:35,519] [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_002694825.1	s__UBA11606 sp002694825	79.823	290	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	97.28	96.77	0.84	0.81	7	-
GCA_002699625.1	s__UBA11606 sp002699625	79.2946	245	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729125.1	s__UBA11606 sp002729125	79.2778	261	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.78	99.78	0.92	0.92	2	-
GCA_016845585.1	s__UBA11606 sp016845585	78.0347	213	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480195.1	s__UBA11606 sp905480195	77.863	176	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699415.1	s__UBA11606 sp018699415	76.8112	95	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__UBA11606	95.0	99.44	99.44	0.86	0.85	3	-
GCA_003697065.1	s__J010 sp003697065	76.5746	116	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.0851	75	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	75.7905	113	641	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:15:35,520] [INFO] GTDB search result was written to OceanDNA-b1781/result_gtdb.tsv
[2023-03-15 08:15:35,521] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:15:35,524] [INFO] DFAST_QC result json was written to OceanDNA-b1781/dqc_result.json
[2023-03-15 08:15:35,524] [INFO] DFAST_QC completed!
[2023-03-15 08:15:35,524] [INFO] Total running time: 0h1m29s