[2023-03-17 09:59:00,864] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,872] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference
[2023-03-17 09:59:02,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,027] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,027] [INFO] Running command: cat /var/lib/cwl/stg96877647-26ce-4c17-b4d0-d69c8d433732/OceanDNA-b24065.fa | prodigal -d OceanDNA-b24065/cds.fna -a OceanDNA-b24065/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:10,389] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:10,389] [INFO] Task started: HMMsearch
[2023-03-17 09:59:10,389] [INFO] Running command: hmmsearch --tblout OceanDNA-b24065/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference/reference_markers.hmm OceanDNA-b24065/protein.faa > /dev/null
[2023-03-17 09:59:10,544] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:10,544] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg96877647-26ce-4c17-b4d0-d69c8d433732/OceanDNA-b24065.fa]
[2023-03-17 09:59:10,639] [INFO] Query marker FASTA was written to OceanDNA-b24065/markers.fasta
[2023-03-17 09:59:10,640] [INFO] Task started: Blastn
[2023-03-17 09:59:10,640] [INFO] Running command: blastn -query OceanDNA-b24065/markers.fasta -db /var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference/reference_markers.fasta -out OceanDNA-b24065/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:11,270] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:11,296] [INFO] Selected 25 target genomes.
[2023-03-17 09:59:11,297] [INFO] Target genome list was writen to OceanDNA-b24065/target_genomes.txt
[2023-03-17 09:59:11,493] [INFO] Task started: fastANI
[2023-03-17 09:59:11,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg96877647-26ce-4c17-b4d0-d69c8d433732/OceanDNA-b24065.fa --refList OceanDNA-b24065/target_genomes.txt --output OceanDNA-b24065/fastani_result.tsv --threads 1
[2023-03-17 09:59:29,208] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:29,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:29,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:29,218] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:59:29,218] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:59:29,218] [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
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.5209	66	450	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.4104	57	450	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.4076	67	450	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.3375	69	450	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.333	79	450	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.3162	81	450	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.244	57	450	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.0649	89	450	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.0575	57	450	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.0393	74	450	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0089	82	450	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.6215	50	450	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.3876	55	450	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:59:29,227] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24065/tc_result.tsv
[2023-03-17 09:59:29,246] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:29,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:29,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference/checkm_data
[2023-03-17 09:59:29,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:29,309] [INFO] Task started: CheckM
[2023-03-17 09:59:29,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24065/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24065/checkm_input OceanDNA-b24065/checkm_result
[2023-03-17 09:59:54,959] [INFO] Task succeeded: CheckM
[2023-03-17 09:59:54,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:59:55,028] [INFO] ===== Completeness check finished =====
[2023-03-17 09:59:55,028] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:59:55,028] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24065/markers.fasta)
[2023-03-17 09:59:55,029] [INFO] Task started: Blastn
[2023-03-17 09:59:55,029] [INFO] Running command: blastn -query OceanDNA-b24065/markers.fasta -db /var/lib/cwl/stgf2428ed4-fef4-4ec2-8861-c0fce1df0c05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24065/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:56,075] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:56,098] [INFO] Selected 21 target genomes.
[2023-03-17 09:59:56,098] [INFO] Target genome list was writen to OceanDNA-b24065/target_genomes_gtdb.txt
[2023-03-17 09:59:56,461] [INFO] Task started: fastANI
[2023-03-17 09:59:56,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg96877647-26ce-4c17-b4d0-d69c8d433732/OceanDNA-b24065.fa --refList OceanDNA-b24065/target_genomes_gtdb.txt --output OceanDNA-b24065/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:00:09,602] [INFO] Task succeeded: fastANI
[2023-03-17 10:00:09,612] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:00:09,613] [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_009377375.1	s__WHUE01 sp009377375	77.6948	170	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	77.0153	68	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.8086	98	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660305.1	s__JABJKO01 sp018660305	76.6304	90	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.5209	66	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870055.1	s__Reyranella sp016870055	76.4309	60	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	76.4078	55	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.3729	57	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	76.3694	59	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187325.1	s__JACPJY01 sp016187325	76.3209	65	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869515.1	s__VGDZ01 sp016869515	76.2959	69	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VGDZ01;f__VGDZ01;g__VGDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.2949	71	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.2071	88	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018729455.1	s__Prosthecomicrobium_A sp018729455	76.0904	52	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Prosthecomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.0649	89	450	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_018401495.1	s__Thalassobaculum_A sp018401495	75.8731	74	450	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_018432935.1	s__JAHDSF01 sp018432935	75.8023	64	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576695.1	s__Nordella sp003576695	75.7198	54	450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__Nordella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:00:09,621] [INFO] GTDB search result was written to OceanDNA-b24065/result_gtdb.tsv
[2023-03-17 10:00:09,641] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:00:09,653] [INFO] DFAST_QC result json was written to OceanDNA-b24065/dqc_result.json
[2023-03-17 10:00:09,654] [INFO] DFAST_QC completed!
[2023-03-17 10:00:09,654] [INFO] Total running time: 0h1m9s