[2023-03-18 03:45:10,278] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,279] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,279] [INFO] DQC Reference Directory: /var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference
[2023-03-18 03:45:12,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,142] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,142] [INFO] Running command: cat /var/lib/cwl/stg60e69dc9-871d-4fe9-84cc-85e92cafcf33/OceanDNA-b22083.fa | prodigal -d OceanDNA-b22083/cds.fna -a OceanDNA-b22083/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:29,344] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:29,344] [INFO] Task started: HMMsearch
[2023-03-18 03:45:29,344] [INFO] Running command: hmmsearch --tblout OceanDNA-b22083/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference/reference_markers.hmm OceanDNA-b22083/protein.faa > /dev/null
[2023-03-18 03:45:29,597] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:29,598] [INFO] Found 6/6 markers.
[2023-03-18 03:45:29,622] [INFO] Query marker FASTA was written to OceanDNA-b22083/markers.fasta
[2023-03-18 03:45:29,622] [INFO] Task started: Blastn
[2023-03-18 03:45:29,622] [INFO] Running command: blastn -query OceanDNA-b22083/markers.fasta -db /var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference/reference_markers.fasta -out OceanDNA-b22083/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:30,272] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:30,273] [INFO] Selected 27 target genomes.
[2023-03-18 03:45:30,273] [INFO] Target genome list was writen to OceanDNA-b22083/target_genomes.txt
[2023-03-18 03:45:30,292] [INFO] Task started: fastANI
[2023-03-18 03:45:30,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e69dc9-871d-4fe9-84cc-85e92cafcf33/OceanDNA-b22083.fa --refList OceanDNA-b22083/target_genomes.txt --output OceanDNA-b22083/fastani_result.tsv --threads 1
[2023-03-18 03:45:57,289] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:57,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:57,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:57,296] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:57,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:57,296] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	77.1687	172	929	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	76.6546	94	929	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	76.6472	93	929	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	76.5597	106	929	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.3807	53	929	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.3766	52	929	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	74.7465	59	929	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:57,296] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22083/tc_result.tsv
[2023-03-18 03:45:57,296] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:57,297] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:57,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference/checkm_data
[2023-03-18 03:45:57,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:57,321] [INFO] Task started: CheckM
[2023-03-18 03:45:57,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22083/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22083/checkm_input OceanDNA-b22083/checkm_result
[2023-03-18 03:46:42,123] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:42,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:42,126] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:42,126] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:42,126] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22083/markers.fasta)
[2023-03-18 03:46:42,126] [INFO] Task started: Blastn
[2023-03-18 03:46:42,126] [INFO] Running command: blastn -query OceanDNA-b22083/markers.fasta -db /var/lib/cwl/stg09b372ff-5562-4551-adcb-3bed2f9886da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22083/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:42,978] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:42,979] [INFO] Selected 30 target genomes.
[2023-03-18 03:46:42,979] [INFO] Target genome list was writen to OceanDNA-b22083/target_genomes_gtdb.txt
[2023-03-18 03:46:43,265] [INFO] Task started: fastANI
[2023-03-18 03:46:43,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg60e69dc9-871d-4fe9-84cc-85e92cafcf33/OceanDNA-b22083.fa --refList OceanDNA-b22083/target_genomes_gtdb.txt --output OceanDNA-b22083/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:47:01,967] [INFO] Task succeeded: fastANI
[2023-03-18 03:47:01,973] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:47:01,974] [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_014207595.1	s__Algisphaera agarilytica	77.1838	171	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284115.1	s__Phycisphaera mikurensis	76.6696	91	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCA_007748075.1	s__Pan265 sp007748075	76.562	106	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Pan265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125285.1	s__RI-212 sp016125285	76.4567	97	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Zrk34;g__RI-212	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119405.1	s__SKPT01 sp007119405	76.4199	73	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__SKPT01	95.0	98.45	98.45	0.84	0.84	2	-
GCA_016125215.1	s__RI-382 sp016125215	76.333	109	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__RI-382	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686995.1	s__GCA-2686995 sp002686995	76.174	96	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__GCA-2686995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551485.1	s__B1Sed10-187 sp003551485	75.9967	68	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__B1Sed10-187	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552605.1	s__B1Sed10-187 sp003552605	75.784	50	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__B1Sed10-187	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015169395.1	s__Humisphaera borealis	75.3807	53	929	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__Humisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:47:01,974] [INFO] GTDB search result was written to OceanDNA-b22083/result_gtdb.tsv
[2023-03-18 03:47:01,974] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:47:01,975] [INFO] DFAST_QC result json was written to OceanDNA-b22083/dqc_result.json
[2023-03-18 03:47:01,975] [INFO] DFAST_QC completed!
[2023-03-18 03:47:01,975] [INFO] Total running time: 0h1m52s