[2023-03-16 16:04:03,877] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:04:03,877] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:04:03,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference
[2023-03-16 16:04:05,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:04:05,205] [INFO] Task started: Prodigal
[2023-03-16 16:04:05,205] [INFO] Running command: cat /var/lib/cwl/stg6d41dadf-66f9-47a8-80c4-c484e09912db/OceanDNA-b32958.fa | prodigal -d OceanDNA-b32958/cds.fna -a OceanDNA-b32958/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:04:24,780] [INFO] Task succeeded: Prodigal
[2023-03-16 16:04:24,780] [INFO] Task started: HMMsearch
[2023-03-16 16:04:24,780] [INFO] Running command: hmmsearch --tblout OceanDNA-b32958/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference/reference_markers.hmm OceanDNA-b32958/protein.faa > /dev/null
[2023-03-16 16:04:25,153] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:04:25,154] [INFO] Found 6/6 markers.
[2023-03-16 16:04:25,179] [INFO] Query marker FASTA was written to OceanDNA-b32958/markers.fasta
[2023-03-16 16:04:25,183] [INFO] Task started: Blastn
[2023-03-16 16:04:25,183] [INFO] Running command: blastn -query OceanDNA-b32958/markers.fasta -db /var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference/reference_markers.fasta -out OceanDNA-b32958/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:04:26,526] [INFO] Task succeeded: Blastn
[2023-03-16 16:04:26,527] [INFO] Selected 30 target genomes.
[2023-03-16 16:04:26,527] [INFO] Target genome list was writen to OceanDNA-b32958/target_genomes.txt
[2023-03-16 16:04:26,544] [INFO] Task started: fastANI
[2023-03-16 16:04:26,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d41dadf-66f9-47a8-80c4-c484e09912db/OceanDNA-b32958.fa --refList OceanDNA-b32958/target_genomes.txt --output OceanDNA-b32958/fastani_result.tsv --threads 1
[2023-03-16 16:04:57,251] [INFO] Task succeeded: fastANI
[2023-03-16 16:04:57,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:04:57,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:04:57,263] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:04:57,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:04:57,263] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.2529	118	881	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.993	99	881	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.9322	96	881	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.8427	52	881	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.7958	90	881	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.7949	102	881	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.7809	116	881	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.7678	83	881	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.7291	81	881	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.6547	71	881	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5995	112	881	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.5709	113	881	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	75.551	91	881	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	75.5113	79	881	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.5108	99	881	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	75.4619	64	881	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.4208	79	881	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	75.4194	60	881	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	75.221	73	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:04:57,263] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32958/tc_result.tsv
[2023-03-16 16:04:57,263] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:04:57,263] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:04:57,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference/checkm_data
[2023-03-16 16:04:57,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:04:57,269] [INFO] Task started: CheckM
[2023-03-16 16:04:57,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32958/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32958/checkm_input OceanDNA-b32958/checkm_result
[2023-03-16 16:05:51,370] [INFO] Task succeeded: CheckM
[2023-03-16 16:05:51,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 16:05:51,373] [INFO] ===== Completeness check finished =====
[2023-03-16 16:05:51,373] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:05:51,373] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32958/markers.fasta)
[2023-03-16 16:05:51,374] [INFO] Task started: Blastn
[2023-03-16 16:05:51,374] [INFO] Running command: blastn -query OceanDNA-b32958/markers.fasta -db /var/lib/cwl/stg67305244-1a31-4c71-b0b4-be14e5e03d7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32958/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:05:52,650] [INFO] Task succeeded: Blastn
[2023-03-16 16:05:52,650] [INFO] Selected 22 target genomes.
[2023-03-16 16:05:52,651] [INFO] Target genome list was writen to OceanDNA-b32958/target_genomes_gtdb.txt
[2023-03-16 16:05:53,421] [INFO] Task started: fastANI
[2023-03-16 16:05:53,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d41dadf-66f9-47a8-80c4-c484e09912db/OceanDNA-b32958.fa --refList OceanDNA-b32958/target_genomes_gtdb.txt --output OceanDNA-b32958/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:06:07,281] [INFO] Task succeeded: fastANI
[2023-03-16 16:06:07,291] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:06:07,292] [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_002937555.1	s__PTKB01 sp002937555	99.2988	586	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018666805.1	s__PTKB01 sp018666805	80.373	592	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	99.32	99.22	0.89	0.88	8	-
GCA_002717225.1	s__PTKB01 sp002717225	76.7517	170	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__PTKB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523425.1	s__WTGU01 sp011523425	76.6977	196	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691045.1	s__SHWC01 sp009691045	76.4639	82	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__SHWC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	75.9897	57	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	75.9802	69	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	75.9778	100	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.9322	96	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.9032	139	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006218045.1	s__Magnetospirillum sp006218045	75.8116	63	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	99.95	99.95	0.98	0.98	2	-
GCF_000423185.1	s__Inquilinus limosus	75.7933	115	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	75.7806	118	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250275.1	s__Alpha-05 sp003250275	75.6962	78	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Alpha-05	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	75.6827	99	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706185.1	s__Roseomonas sp902706185	75.4923	91	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900492205.1	s__Allorhizobium naphthalenivorans_A	75.4304	64	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.27	95.27	0.88	0.88	2	-
GCA_017418605.1	s__CAISGS01 sp017418605	75.3855	82	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__CAISGS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796995.1	s__Allorhizobium sp002796995	75.3799	74	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.22	96.20	0.94	0.93	7	-
--------------------------------------------------------------------------------
[2023-03-16 16:06:07,292] [INFO] GTDB search result was written to OceanDNA-b32958/result_gtdb.tsv
[2023-03-16 16:06:07,292] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:06:07,294] [INFO] DFAST_QC result json was written to OceanDNA-b32958/dqc_result.json
[2023-03-16 16:06:07,294] [INFO] DFAST_QC completed!
[2023-03-16 16:06:07,294] [INFO] Total running time: 0h2m3s