[2023-03-15 03:35:14,985] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:35:14,986] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:35:14,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference
[2023-03-15 03:35:16,524] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:35:16,525] [INFO] Task started: Prodigal
[2023-03-15 03:35:16,525] [INFO] Running command: cat /var/lib/cwl/stg70c34b5c-10c8-4956-b732-57aae64607b9/OceanDNA-b30009.fa | prodigal -d OceanDNA-b30009/cds.fna -a OceanDNA-b30009/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:35:38,382] [INFO] Task succeeded: Prodigal
[2023-03-15 03:35:38,382] [INFO] Task started: HMMsearch
[2023-03-15 03:35:38,382] [INFO] Running command: hmmsearch --tblout OceanDNA-b30009/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference/reference_markers.hmm OceanDNA-b30009/protein.faa > /dev/null
[2023-03-15 03:35:38,610] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:35:38,610] [INFO] Found 6/6 markers.
[2023-03-15 03:35:38,641] [INFO] Query marker FASTA was written to OceanDNA-b30009/markers.fasta
[2023-03-15 03:35:38,642] [INFO] Task started: Blastn
[2023-03-15 03:35:38,642] [INFO] Running command: blastn -query OceanDNA-b30009/markers.fasta -db /var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference/reference_markers.fasta -out OceanDNA-b30009/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:35:39,516] [INFO] Task succeeded: Blastn
[2023-03-15 03:35:39,516] [INFO] Selected 21 target genomes.
[2023-03-15 03:35:39,517] [INFO] Target genome list was writen to OceanDNA-b30009/target_genomes.txt
[2023-03-15 03:35:39,529] [INFO] Task started: fastANI
[2023-03-15 03:35:39,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c34b5c-10c8-4956-b732-57aae64607b9/OceanDNA-b30009.fa --refList OceanDNA-b30009/target_genomes.txt --output OceanDNA-b30009/fastani_result.tsv --threads 1
[2023-03-15 03:35:57,305] [INFO] Task succeeded: fastANI
[2023-03-15 03:35:57,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:35:57,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:35:57,318] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 03:35:57,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 03:35:57,318] [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
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	98.8913	1156	1218	95	conclusive
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	98.8843	1156	1218	95	conclusive
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	80.1583	579	1218	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	79.914	519	1218	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.8022	585	1218	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	79.7104	565	1218	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.6168	558	1218	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.5374	501	1218	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	79.4338	548	1218	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	79.399	556	1218	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.3901	555	1218	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.3553	555	1218	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.9161	429	1218	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	78.9109	432	1218	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.7412	403	1218	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	78.7267	399	1218	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.6863	429	1218	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.3938	368	1218	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.1667	315	1218	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.9291	342	1218	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.8872	331	1218	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:35:57,318] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30009/tc_result.tsv
[2023-03-15 03:35:57,318] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:35:57,318] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:35:57,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference/checkm_data
[2023-03-15 03:35:57,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:35:57,331] [INFO] Task started: CheckM
[2023-03-15 03:35:57,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30009/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30009/checkm_input OceanDNA-b30009/checkm_result
[2023-03-15 03:36:52,092] [INFO] Task succeeded: CheckM
[2023-03-15 03:36:52,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:36:52,095] [INFO] ===== Completeness check finished =====
[2023-03-15 03:36:52,095] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:36:52,096] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30009/markers.fasta)
[2023-03-15 03:36:52,102] [INFO] Task started: Blastn
[2023-03-15 03:36:52,102] [INFO] Running command: blastn -query OceanDNA-b30009/markers.fasta -db /var/lib/cwl/stg859b6436-8d9b-4329-81df-5eb51ca97c9d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30009/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:36:53,679] [INFO] Task succeeded: Blastn
[2023-03-15 03:36:53,680] [INFO] Selected 21 target genomes.
[2023-03-15 03:36:53,680] [INFO] Target genome list was writen to OceanDNA-b30009/target_genomes_gtdb.txt
[2023-03-15 03:36:53,746] [INFO] Task started: fastANI
[2023-03-15 03:36:53,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg70c34b5c-10c8-4956-b732-57aae64607b9/OceanDNA-b30009.fa --refList OceanDNA-b30009/target_genomes_gtdb.txt --output OceanDNA-b30009/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:37:13,861] [INFO] Task succeeded: fastANI
[2023-03-15 03:37:13,873] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:37:13,873] [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_000688295.1	s__Pseudooceanicola nanhaiensis	98.8913	1156	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002210105.1	s__Pseudooceanicola sp002210105	83.3599	829	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	82.6296	515	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152725.1	s__Pseudooceanicola batsensis	80.9723	632	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638275.1	s__Pseudooceanicola flagellatus	80.9423	626	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	80.053	597	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	79.9178	517	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_002300555.1	s__Salipiger sp002300555	79.8496	415	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	79.8108	584	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	79.79	532	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.6959	542	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959925.1	s__Pseudooceanicola onchidii	79.6335	557	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656415.1	s__Seohaeicola zhoushanensis	79.5657	603	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Seohaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109195.1	s__Pseudooceanicola nitratireducens	79.4403	546	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	98.54	97.09	0.97	0.95	3	-
GCF_900116195.1	s__Salipiger pacificus	79.3588	555	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900107235.1	s__Citreimonas salinaria	79.2774	473	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	79.1234	510	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_003590145.2	s__Pseudooceanicola algae	78.8903	434	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	78.8074	416	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106675.1	s__Acidimangrovimonas indica	78.7153	400	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCA_002709085.1	s__Pseudooceanicola sp002709085	78.1617	309	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:37:13,874] [INFO] GTDB search result was written to OceanDNA-b30009/result_gtdb.tsv
[2023-03-15 03:37:13,874] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:37:13,877] [INFO] DFAST_QC result json was written to OceanDNA-b30009/dqc_result.json
[2023-03-15 03:37:13,877] [INFO] DFAST_QC completed!
[2023-03-15 03:37:13,877] [INFO] Total running time: 0h1m59s