[2023-03-14 11:49:37,370] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:37,377] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:37,377] [INFO] DQC Reference Directory: /var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference
[2023-03-14 11:49:38,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:38,964] [INFO] Task started: Prodigal
[2023-03-14 11:49:38,964] [INFO] Running command: cat /var/lib/cwl/stg550d0e58-2ab4-4235-99c1-eb949234bb48/OceanDNA-b11036.fa | prodigal -d OceanDNA-b11036/cds.fna -a OceanDNA-b11036/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:56,562] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:56,562] [INFO] Task started: HMMsearch
[2023-03-14 11:49:56,562] [INFO] Running command: hmmsearch --tblout OceanDNA-b11036/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference/reference_markers.hmm OceanDNA-b11036/protein.faa > /dev/null
[2023-03-14 11:49:56,750] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:56,751] [INFO] Found 6/6 markers.
[2023-03-14 11:49:56,823] [INFO] Query marker FASTA was written to OceanDNA-b11036/markers.fasta
[2023-03-14 11:49:56,824] [INFO] Task started: Blastn
[2023-03-14 11:49:56,824] [INFO] Running command: blastn -query OceanDNA-b11036/markers.fasta -db /var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference/reference_markers.fasta -out OceanDNA-b11036/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:57,402] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:57,426] [INFO] Selected 21 target genomes.
[2023-03-14 11:49:57,426] [INFO] Target genome list was writen to OceanDNA-b11036/target_genomes.txt
[2023-03-14 11:49:57,441] [INFO] Task started: fastANI
[2023-03-14 11:49:57,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg550d0e58-2ab4-4235-99c1-eb949234bb48/OceanDNA-b11036.fa --refList OceanDNA-b11036/target_genomes.txt --output OceanDNA-b11036/fastani_result.tsv --threads 1
[2023-03-14 11:50:09,687] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:09,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:50:09,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:50:09,699] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:50:09,699] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:50:09,699] [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
Flavicella marina	strain=2A-7	GCA_009193215.1	1475951	1475951	type	True	79.8751	397	872	95	below_threshold
Flavicella sediminum	strain=ALS 84	GCA_006381105.1	2585141	2585141	type	True	78.6311	306	872	95	below_threshold
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	77.563	149	872	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	77.4698	155	872	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	77.3445	158	872	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	77.0358	130	872	95	below_threshold
Polaribacter pacificus	strain=CGMCC 1.15763	GCA_014643655.1	1775173	1775173	type	True	76.9951	73	872	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.8408	137	872	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.6658	145	872	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	76.5729	150	872	95	below_threshold
Tenacibaculum mesophilum	strain=DSM 13764	GCA_009362255.1	104268	104268	type	True	76.5503	89	872	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	76.4864	120	872	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.3871	128	872	95	below_threshold
Aureivirga marina	strain=LMG 26721	GCA_015767265.1	1182451	1182451	type	True	76.3561	112	872	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.3221	109	872	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.3082	111	872	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.3047	110	872	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.1617	73	872	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	75.8509	77	872	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:50:09,701] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11036/tc_result.tsv
[2023-03-14 11:50:09,703] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:50:09,703] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:50:09,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference/checkm_data
[2023-03-14 11:50:09,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:50:09,801] [INFO] Task started: CheckM
[2023-03-14 11:50:09,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11036/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11036/checkm_input OceanDNA-b11036/checkm_result
[2023-03-14 11:50:56,072] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:56,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:56,162] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:56,162] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:56,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11036/markers.fasta)
[2023-03-14 11:50:56,164] [INFO] Task started: Blastn
[2023-03-14 11:50:56,164] [INFO] Running command: blastn -query OceanDNA-b11036/markers.fasta -db /var/lib/cwl/stg591623c1-2a17-45d6-b22f-85d76e085d05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11036/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:57,014] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:57,051] [INFO] Selected 19 target genomes.
[2023-03-14 11:50:57,052] [INFO] Target genome list was writen to OceanDNA-b11036/target_genomes_gtdb.txt
[2023-03-14 11:50:57,106] [INFO] Task started: fastANI
[2023-03-14 11:50:57,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg550d0e58-2ab4-4235-99c1-eb949234bb48/OceanDNA-b11036.fa --refList OceanDNA-b11036/target_genomes_gtdb.txt --output OceanDNA-b11036/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:51:06,802] [INFO] Task succeeded: fastANI
[2023-03-14 11:51:06,812] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:51:06,812] [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_009193215.1	s__Flavicella marina	79.862	398	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006381105.1	s__Flavicella sediminum	78.6253	307	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479475.1	s__Flavicella sp905479475	77.6645	139	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927765.1	s__Wenyingzhuangia aestuarii	77.5625	150	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	77.4744	156	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	77.3456	159	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477565.1	s__Flavicella sp002477565	77.3263	82	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavicella	95.0	98.32	98.32	0.91	0.91	2	-
GCF_002814075.1	s__Polaribacter sejongensis	77.032	129	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCA_001874265.1	s__Urechidicola sp001874265	76.74	94	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827455.1	s__VISM01 sp007827455	76.7122	121	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__VISM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019263805.1	s__Polaribacter sp011379025	76.6796	117	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	98.52	98.52	0.95	0.95	2	-
GCF_002954605.1	s__Polaribacter butkevichii	76.6716	146	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000766795.1	s__Polaribacter sp000766795	76.6487	156	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	76.4885	121	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009832745.1	s__Polaribacter sp009832745	76.372	129	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.3047	110	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012524075.1	s__Lutibacter sp012524075	76.2296	92	872	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:51:06,826] [INFO] GTDB search result was written to OceanDNA-b11036/result_gtdb.tsv
[2023-03-14 11:51:06,850] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:51:06,863] [INFO] DFAST_QC result json was written to OceanDNA-b11036/dqc_result.json
[2023-03-14 11:51:06,863] [INFO] DFAST_QC completed!
[2023-03-14 11:51:06,863] [INFO] Total running time: 0h1m29s