[2023-03-19 01:55:26,702] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:55:26,703] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:55:26,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference
[2023-03-19 01:55:27,787] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:55:27,787] [INFO] Task started: Prodigal
[2023-03-19 01:55:27,787] [INFO] Running command: cat /var/lib/cwl/stg65a249df-62fc-4a49-8287-b50946c18768/OceanDNA-b23012.fa | prodigal -d OceanDNA-b23012/cds.fna -a OceanDNA-b23012/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:56:04,513] [INFO] Task succeeded: Prodigal
[2023-03-19 01:56:04,514] [INFO] Task started: HMMsearch
[2023-03-19 01:56:04,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b23012/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference/reference_markers.hmm OceanDNA-b23012/protein.faa > /dev/null
[2023-03-19 01:56:04,750] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:56:04,750] [INFO] Found 6/6 markers.
[2023-03-19 01:56:04,793] [INFO] Query marker FASTA was written to OceanDNA-b23012/markers.fasta
[2023-03-19 01:56:04,794] [INFO] Task started: Blastn
[2023-03-19 01:56:04,794] [INFO] Running command: blastn -query OceanDNA-b23012/markers.fasta -db /var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference/reference_markers.fasta -out OceanDNA-b23012/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:56:05,405] [INFO] Task succeeded: Blastn
[2023-03-19 01:56:05,413] [INFO] Selected 24 target genomes.
[2023-03-19 01:56:05,414] [INFO] Target genome list was writen to OceanDNA-b23012/target_genomes.txt
[2023-03-19 01:56:05,428] [INFO] Task started: fastANI
[2023-03-19 01:56:05,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a249df-62fc-4a49-8287-b50946c18768/OceanDNA-b23012.fa --refList OceanDNA-b23012/target_genomes.txt --output OceanDNA-b23012/fastani_result.tsv --threads 1
[2023-03-19 01:56:22,996] [INFO] Task succeeded: fastANI
[2023-03-19 01:56:22,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:56:22,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:56:23,010] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:56:23,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:56:23,011] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.3594	59	2053	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.1954	98	2053	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	75.1404	70	2053	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.0605	91	2053	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	75.0233	115	2053	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	74.9839	115	2053	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.9702	128	2053	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	74.8858	116	2053	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	74.8661	152	2053	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	74.8619	124	2053	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8532	181	2053	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.8457	174	2053	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	74.8317	138	2053	95	below_threshold
Xanthomonas citri	strain=LMG712	GCA_002019125.1	346	346	pathovar	True	74.7691	58	2053	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	74.7676	69	2053	95	below_threshold
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	74.7666	59	2053	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.7653	146	2053	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	74.7642	137	2053	95	below_threshold
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	74.7457	58	2053	95	below_threshold
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	74.7424	59	2053	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.7391	151	2053	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.7357	130	2053	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	74.7162	155	2053	95	below_threshold
Brevibacterium rongguiense	strain=5221	GCA_009857845.1	2695267	2695267	type	True	74.6883	102	2053	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:56:23,011] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23012/tc_result.tsv
[2023-03-19 01:56:23,011] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:56:23,011] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:56:23,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference/checkm_data
[2023-03-19 01:56:23,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:56:23,022] [INFO] Task started: CheckM
[2023-03-19 01:56:23,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23012/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23012/checkm_input OceanDNA-b23012/checkm_result
[2023-03-19 01:57:48,632] [INFO] Task succeeded: CheckM
[2023-03-19 01:57:48,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:57:48,636] [INFO] ===== Completeness check finished =====
[2023-03-19 01:57:48,637] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:57:48,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23012/markers.fasta)
[2023-03-19 01:57:48,638] [INFO] Task started: Blastn
[2023-03-19 01:57:48,638] [INFO] Running command: blastn -query OceanDNA-b23012/markers.fasta -db /var/lib/cwl/stg447b4b1d-26b4-4b25-b46e-a7030f21e1a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23012/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:57:49,600] [INFO] Task succeeded: Blastn
[2023-03-19 01:57:49,601] [INFO] Selected 17 target genomes.
[2023-03-19 01:57:49,601] [INFO] Target genome list was writen to OceanDNA-b23012/target_genomes_gtdb.txt
[2023-03-19 01:57:49,617] [INFO] Task started: fastANI
[2023-03-19 01:57:49,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a249df-62fc-4a49-8287-b50946c18768/OceanDNA-b23012.fa --refList OceanDNA-b23012/target_genomes_gtdb.txt --output OceanDNA-b23012/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:58:05,401] [INFO] Task succeeded: fastANI
[2023-03-19 01:58:05,411] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:58:05,412] [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_016709875.1	s__JADJLZ01 sp016709875	77.6542	482	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	77.1167	396	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_016872755.1	s__GW928-bin9 sp016872755	77.0531	325	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	77.0345	336	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712565.1	s__JADJQU01 sp016712565	76.8867	309	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	76.8713	458	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.8676	457	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.8156	502	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	76.8023	505	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	76.7605	564	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751255.1	s__Pla86 sp007751255	76.6433	380	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016220035.1	s__JADJNY01 sp016220035	76.612	410	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903829565.1	s__SXXH01 sp903829565	76.5327	115	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	98.11	97.95	0.77	0.75	5	-
GCA_004296785.1	s__GW928-bin9 sp004296785	76.4809	346	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	76.4749	306	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	76.4213	357	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789645.1	s__SXXH01 sp005789645	76.4147	227	2053	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	99.62	99.60	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-19 01:58:05,412] [INFO] GTDB search result was written to OceanDNA-b23012/result_gtdb.tsv
[2023-03-19 01:58:05,412] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:58:05,414] [INFO] DFAST_QC result json was written to OceanDNA-b23012/dqc_result.json
[2023-03-19 01:58:05,414] [INFO] DFAST_QC completed!
[2023-03-19 01:58:05,414] [INFO] Total running time: 0h2m39s