[2023-03-17 01:23:45,162] [INFO] DFAST_QC pipeline started.
[2023-03-17 01:23:45,162] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 01:23:45,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference
[2023-03-17 01:23:46,317] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 01:23:46,317] [INFO] Task started: Prodigal
[2023-03-17 01:23:46,317] [INFO] Running command: cat /var/lib/cwl/stg4618ab57-5e8b-4f38-bffc-49f5787f97f2/OceanDNA-a828.fa | prodigal -d OceanDNA-a828/cds.fna -a OceanDNA-a828/protein.faa -g 11 -q > /dev/null
[2023-03-17 01:23:50,956] [INFO] Task succeeded: Prodigal
[2023-03-17 01:23:50,956] [INFO] Task started: HMMsearch
[2023-03-17 01:23:50,956] [INFO] Running command: hmmsearch --tblout OceanDNA-a828/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference/reference_markers.hmm OceanDNA-a828/protein.faa > /dev/null
[2023-03-17 01:23:51,060] [INFO] Task succeeded: HMMsearch
[2023-03-17 01:23:51,060] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg4618ab57-5e8b-4f38-bffc-49f5787f97f2/OceanDNA-a828.fa]
[2023-03-17 01:23:51,069] [INFO] Query marker FASTA was written to OceanDNA-a828/markers.fasta
[2023-03-17 01:23:51,069] [INFO] Task started: Blastn
[2023-03-17 01:23:51,069] [INFO] Running command: blastn -query OceanDNA-a828/markers.fasta -db /var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference/reference_markers.fasta -out OceanDNA-a828/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:23:51,487] [INFO] Task succeeded: Blastn
[2023-03-17 01:23:51,487] [INFO] Selected 5 target genomes.
[2023-03-17 01:23:51,487] [INFO] Target genome list was writen to OceanDNA-a828/target_genomes.txt
[2023-03-17 01:23:51,490] [INFO] Task started: fastANI
[2023-03-17 01:23:51,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg4618ab57-5e8b-4f38-bffc-49f5787f97f2/OceanDNA-a828.fa --refList OceanDNA-a828/target_genomes.txt --output OceanDNA-a828/fastani_result.tsv --threads 1
[2023-03-17 01:23:53,052] [INFO] Task succeeded: fastANI
[2023-03-17 01:23:53,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 01:23:53,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 01:23:53,183] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 01:23:53,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 01:23:53,183] [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
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	81.5175	229	287	95	below_threshold
Nitrosopumilus cobalaminigenes	strain=HCA1	GCA_013407145.1	1470066	1470066	type	True	81.4806	236	287	95	below_threshold
Nitrosopumilus adriaticus	strain=NF5	GCA_000956175.1	1580092	1580092	type	True	80.7454	217	287	95	below_threshold
Nitrosopumilus maritimus	strain=SCM1	GCA_000018465.1	338192	338192	type	True	80.5653	217	287	95	below_threshold
Nitrosopumilus ureiphilus	strain=PS0	GCA_013407185.1	1470067	1470067	type	True	80.4127	222	287	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 01:23:53,183] [INFO] DFAST Taxonomy check result was written to OceanDNA-a828/tc_result.tsv
[2023-03-17 01:23:53,184] [INFO] ===== Taxonomy check completed =====
[2023-03-17 01:23:53,184] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 01:23:53,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference/checkm_data
[2023-03-17 01:23:53,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 01:23:53,186] [INFO] Task started: CheckM
[2023-03-17 01:23:53,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a828/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a828/checkm_input OceanDNA-a828/checkm_result
[2023-03-17 01:24:13,935] [INFO] Task succeeded: CheckM
[2023-03-17 01:24:13,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 01:24:13,936] [INFO] ===== Completeness check finished =====
[2023-03-17 01:24:13,937] [INFO] ===== Start GTDB Search =====
[2023-03-17 01:24:13,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a828/markers.fasta)
[2023-03-17 01:24:13,940] [INFO] Task started: Blastn
[2023-03-17 01:24:13,940] [INFO] Running command: blastn -query OceanDNA-a828/markers.fasta -db /var/lib/cwl/stgf2a027b5-d8b5-4d12-8e46-f6bcf090914c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a828/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 01:24:14,560] [INFO] Task succeeded: Blastn
[2023-03-17 01:24:14,561] [INFO] Selected 5 target genomes.
[2023-03-17 01:24:14,561] [INFO] Target genome list was writen to OceanDNA-a828/target_genomes_gtdb.txt
[2023-03-17 01:24:14,683] [INFO] Task started: fastANI
[2023-03-17 01:24:14,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg4618ab57-5e8b-4f38-bffc-49f5787f97f2/OceanDNA-a828.fa --refList OceanDNA-a828/target_genomes_gtdb.txt --output OceanDNA-a828/fastani_result_gtdb.tsv --threads 1
[2023-03-17 01:24:16,010] [INFO] Task succeeded: fastANI
[2023-03-17 01:24:16,013] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 01:24:16,014] [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_003331425.1	s__Nitrosopumilus sp002690535	99.5055	283	287	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	99.22	99.22	0.96	0.96	2	conclusive
GCF_002156965.1	s__Nitrosopumilus catalinensis	93.9659	280	287	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	96.25	96.25	1.00	1.00	2	-
GCA_013867245.1	s__Nitrosopumilus sp013867245	90.395	172	287	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001541925.1	s__Nitrosopumilus sp001541925	90.3492	267	287	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003702465.1	s__Nitrosopumilus sp003702465	89.4228	239	287	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 01:24:16,014] [INFO] GTDB search result was written to OceanDNA-a828/result_gtdb.tsv
[2023-03-17 01:24:16,014] [INFO] ===== GTDB Search completed =====
[2023-03-17 01:24:16,015] [INFO] DFAST_QC result json was written to OceanDNA-a828/dqc_result.json
[2023-03-17 01:24:16,015] [INFO] DFAST_QC completed!
[2023-03-17 01:24:16,015] [INFO] Total running time: 0h0m31s