[2023-03-16 06:46:39,279] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:46:39,279] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:46:39,280] [INFO] DQC Reference Directory: /var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference
[2023-03-16 06:46:40,378] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:46:40,379] [INFO] Task started: Prodigal
[2023-03-16 06:46:40,379] [INFO] Running command: cat /var/lib/cwl/stg86503d67-ccd9-4601-b306-4f285c7f6fbe/OceanDNA-b38208.fa | prodigal -d OceanDNA-b38208/cds.fna -a OceanDNA-b38208/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:46:59,431] [INFO] Task succeeded: Prodigal
[2023-03-16 06:46:59,432] [INFO] Task started: HMMsearch
[2023-03-16 06:46:59,432] [INFO] Running command: hmmsearch --tblout OceanDNA-b38208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference/reference_markers.hmm OceanDNA-b38208/protein.faa > /dev/null
[2023-03-16 06:46:59,639] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:46:59,639] [INFO] Found 6/6 markers.
[2023-03-16 06:46:59,664] [INFO] Query marker FASTA was written to OceanDNA-b38208/markers.fasta
[2023-03-16 06:46:59,665] [INFO] Task started: Blastn
[2023-03-16 06:46:59,665] [INFO] Running command: blastn -query OceanDNA-b38208/markers.fasta -db /var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference/reference_markers.fasta -out OceanDNA-b38208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:47:00,483] [INFO] Task succeeded: Blastn
[2023-03-16 06:47:00,484] [INFO] Selected 23 target genomes.
[2023-03-16 06:47:00,484] [INFO] Target genome list was writen to OceanDNA-b38208/target_genomes.txt
[2023-03-16 06:47:00,555] [INFO] Task started: fastANI
[2023-03-16 06:47:00,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg86503d67-ccd9-4601-b306-4f285c7f6fbe/OceanDNA-b38208.fa --refList OceanDNA-b38208/target_genomes.txt --output OceanDNA-b38208/fastani_result.tsv --threads 1
[2023-03-16 06:47:16,292] [INFO] Task succeeded: fastANI
[2023-03-16 06:47:16,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:47:16,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:47:16,306] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 06:47:16,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 06:47:16,306] [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
Cobetia marina	strain=JCM 21022	GCA_001720485.1	28258	28258	type	True	98.4792	864	922	95	conclusive
Cobetia crustatorum	strain=JO1	GCA_000591415.1	553385	553385	type	True	83.8307	683	922	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.3872	332	922	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.1897	335	922	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	78.771	320	922	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	78.7108	331	922	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	78.6384	321	922	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.6346	324	922	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	78.6101	303	922	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	78.5788	343	922	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.5747	244	922	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	78.5574	244	922	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	78.516	316	922	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	78.5133	299	922	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	78.5053	314	922	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.4975	298	922	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.4887	287	922	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.4265	283	922	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	78.3721	295	922	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	78.3047	295	922	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.209	275	922	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	78.2072	313	922	95	below_threshold
Halomonas saliphila	strain=LCB169	GCA_002930105.1	1848458	1848458	type	True	78.0267	256	922	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:47:16,360] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38208/tc_result.tsv
[2023-03-16 06:47:16,360] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:47:16,360] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:47:16,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference/checkm_data
[2023-03-16 06:47:16,361] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:47:16,403] [INFO] Task started: CheckM
[2023-03-16 06:47:16,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38208/checkm_input OceanDNA-b38208/checkm_result
[2023-03-16 06:48:07,713] [INFO] Task succeeded: CheckM
[2023-03-16 06:48:07,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:48:07,717] [INFO] ===== Completeness check finished =====
[2023-03-16 06:48:07,717] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:48:07,717] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38208/markers.fasta)
[2023-03-16 06:48:07,718] [INFO] Task started: Blastn
[2023-03-16 06:48:07,718] [INFO] Running command: blastn -query OceanDNA-b38208/markers.fasta -db /var/lib/cwl/stg16590159-6fac-41b0-9e59-ddc7b653d8f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:48:09,074] [INFO] Task succeeded: Blastn
[2023-03-16 06:48:09,075] [INFO] Selected 13 target genomes.
[2023-03-16 06:48:09,075] [INFO] Target genome list was writen to OceanDNA-b38208/target_genomes_gtdb.txt
[2023-03-16 06:48:09,192] [INFO] Task started: fastANI
[2023-03-16 06:48:09,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg86503d67-ccd9-4601-b306-4f285c7f6fbe/OceanDNA-b38208.fa --refList OceanDNA-b38208/target_genomes_gtdb.txt --output OceanDNA-b38208/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:48:18,557] [INFO] Task succeeded: fastANI
[2023-03-16 06:48:18,565] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:48:18,565] [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_001720485.1	s__Cobetia marina	98.4792	864	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.51	98.31	0.95	0.93	9	conclusive
GCF_000754225.1	s__Cobetia amphilecti	88.6476	798	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	96.77	95.09	0.91	0.86	19	-
GCF_000591415.1	s__Cobetia crustatorum	83.848	682	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	98.71	98.71	0.93	0.93	2	-
GCF_009796845.1	s__Cobetia sp009796845	82.8256	699	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Cobetia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	79.3577	334	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	79.1751	336	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCA_001577635.1	s__Halomonas_C sp001577635	78.919	324	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117855.1	s__Halomonas_C coralii	78.6707	338	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	78.579	342	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645095.1	s__Halomonas_F sp015645095	78.3995	307	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	78.3757	236	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102875.1	s__Halomonas_B pantelleriensis	78.3588	296	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900961225.1	s__Halomonas_C sp900961225	78.3541	315	922	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:48:18,566] [INFO] GTDB search result was written to OceanDNA-b38208/result_gtdb.tsv
[2023-03-16 06:48:18,566] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:48:18,568] [INFO] DFAST_QC result json was written to OceanDNA-b38208/dqc_result.json
[2023-03-16 06:48:18,568] [INFO] DFAST_QC completed!
[2023-03-16 06:48:18,568] [INFO] Total running time: 0h1m39s