[2023-03-18 10:12:10,202] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:12:10,202] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:12:10,202] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference
[2023-03-18 10:12:11,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:12:11,302] [INFO] Task started: Prodigal
[2023-03-18 10:12:11,302] [INFO] Running command: cat /var/lib/cwl/stgfc30ffa0-4ede-4cfa-aedb-ad58f048a380/OceanDNA-b36079.fa | prodigal -d OceanDNA-b36079/cds.fna -a OceanDNA-b36079/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:12:27,783] [INFO] Task succeeded: Prodigal
[2023-03-18 10:12:27,784] [INFO] Task started: HMMsearch
[2023-03-18 10:12:27,784] [INFO] Running command: hmmsearch --tblout OceanDNA-b36079/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference/reference_markers.hmm OceanDNA-b36079/protein.faa > /dev/null
[2023-03-18 10:12:27,975] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:12:27,976] [INFO] Found 6/6 markers.
[2023-03-18 10:12:27,999] [INFO] Query marker FASTA was written to OceanDNA-b36079/markers.fasta
[2023-03-18 10:12:27,999] [INFO] Task started: Blastn
[2023-03-18 10:12:27,999] [INFO] Running command: blastn -query OceanDNA-b36079/markers.fasta -db /var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference/reference_markers.fasta -out OceanDNA-b36079/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:12:28,731] [INFO] Task succeeded: Blastn
[2023-03-18 10:12:28,734] [INFO] Selected 33 target genomes.
[2023-03-18 10:12:28,734] [INFO] Target genome list was writen to OceanDNA-b36079/target_genomes.txt
[2023-03-18 10:12:28,754] [INFO] Task started: fastANI
[2023-03-18 10:12:28,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc30ffa0-4ede-4cfa-aedb-ad58f048a380/OceanDNA-b36079.fa --refList OceanDNA-b36079/target_genomes.txt --output OceanDNA-b36079/fastani_result.tsv --threads 1
[2023-03-18 10:12:48,599] [INFO] Task succeeded: fastANI
[2023-03-18 10:12:48,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:12:48,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:12:48,613] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:12:48,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:12:48,614] [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
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	78.97	409	851	95	below_threshold
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	77.101	173	851	95	below_threshold
Nevskia soli	strain=DSM 19509	GCA_000711955.1	418856	418856	type	True	77.0494	148	851	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	76.9764	137	851	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	76.7323	120	851	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.6564	171	851	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	76.6287	127	851	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	76.5425	135	851	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	76.5365	102	851	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	76.4918	120	851	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.4649	181	851	95	below_threshold
Nevskia ramosa	strain=DSM 11499	GCA_000420645.1	64002	64002	type	True	76.4204	104	851	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	76.3135	74	851	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	76.2649	77	851	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.2474	70	851	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	76.2169	78	851	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.1488	64	851	95	below_threshold
Vulcaniibacterium thermophilum	strain=KCTC 32020	GCA_007923255.1	1169913	1169913	type	True	76.1306	67	851	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	76.1283	67	851	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.1124	75	851	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	76.102	97	851	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	76.0389	68	851	95	below_threshold
Lysobacter psychrotolerans	strain=ZS60	GCA_003719825.1	1327343	1327343	type	True	76.0051	51	851	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.0033	86	851	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	75.8751	60	851	95	below_threshold
Arenimonas oryziterrae	strain=DSM 21050	GCA_000420545.1	498055	498055	type	True	75.5864	56	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:12:48,615] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36079/tc_result.tsv
[2023-03-18 10:12:48,616] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:12:48,616] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:12:48,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference/checkm_data
[2023-03-18 10:12:48,617] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:12:48,645] [INFO] Task started: CheckM
[2023-03-18 10:12:48,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36079/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36079/checkm_input OceanDNA-b36079/checkm_result
[2023-03-18 10:13:31,510] [INFO] Task succeeded: CheckM
[2023-03-18 10:13:31,511] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 10:13:31,514] [INFO] ===== Completeness check finished =====
[2023-03-18 10:13:31,514] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:13:31,514] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36079/markers.fasta)
[2023-03-18 10:13:31,515] [INFO] Task started: Blastn
[2023-03-18 10:13:31,515] [INFO] Running command: blastn -query OceanDNA-b36079/markers.fasta -db /var/lib/cwl/stg3f953923-220a-4846-8b43-aa4bd9cac760/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36079/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:13:32,774] [INFO] Task succeeded: Blastn
[2023-03-18 10:13:32,777] [INFO] Selected 30 target genomes.
[2023-03-18 10:13:32,777] [INFO] Target genome list was writen to OceanDNA-b36079/target_genomes_gtdb.txt
[2023-03-18 10:13:32,858] [INFO] Task started: fastANI
[2023-03-18 10:13:32,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc30ffa0-4ede-4cfa-aedb-ad58f048a380/OceanDNA-b36079.fa --refList OceanDNA-b36079/target_genomes_gtdb.txt --output OceanDNA-b36079/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:13:53,040] [INFO] Task succeeded: fastANI
[2023-03-18 10:13:53,055] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:13:53,055] [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_000733765.1	s__Algiphilus aromaticivorans	79.0038	406	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Algiphilaceae;g__Algiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	77.1306	113	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	77.015	135	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706265.1	s__Polycyclovorans sp002706265	76.9323	103	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	99.22	98.54	0.87	0.78	3	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	76.9269	161	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	76.7261	143	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	76.7183	170	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	76.6952	168	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_012241385.1	s__Solimonas marina	76.6648	125	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	76.5587	134	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	76.5558	175	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711245.1	s__Polycyclovorans algicola	76.5365	102	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	76.4851	178	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_011058255.1	s__XN24 sp011058255	76.4268	68	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823855.1	s__Nevskia sp013823855	76.3765	116	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	76.2747	69	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416885.1	s__Luteimonas_B sp003416885	76.2649	77	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641285.1	s__Dyella_A thiooxydans	76.2182	78	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113085.1	s__Fontimonas thermophila	76.2014	102	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Fontimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	76.1488	64	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302295.1	s__Thauera sp017302295	76.0755	52	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	75.9969	91	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002799155.1	s__Stenotrophomonas maltophilia_R	75.6371	57	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284595.1	s__Stenotrophomonas maltophilia_F	75.518	79	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.76	98.38	0.92	0.88	60	-
GCA_001464385.1	s__Ga0077550 sp001464385	74.8834	56	851	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	74.8207	74	851	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_016793465.1	s__Nannocystis sp016793465	74.7636	60	851	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:13:53,056] [INFO] GTDB search result was written to OceanDNA-b36079/result_gtdb.tsv
[2023-03-18 10:13:53,056] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:13:53,059] [INFO] DFAST_QC result json was written to OceanDNA-b36079/dqc_result.json
[2023-03-18 10:13:53,059] [INFO] DFAST_QC completed!
[2023-03-18 10:13:53,059] [INFO] Total running time: 0h1m43s