[2023-03-18 22:02:41,370] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:02:41,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:02:41,370] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference
[2023-03-18 22:02:42,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:02:42,498] [INFO] Task started: Prodigal
[2023-03-18 22:02:42,498] [INFO] Running command: cat /var/lib/cwl/stg67f48c7e-8b57-4051-979d-72d6cd70765c/OceanDNA-b22256.fa | prodigal -d OceanDNA-b22256/cds.fna -a OceanDNA-b22256/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:02:57,604] [INFO] Task succeeded: Prodigal
[2023-03-18 22:02:57,605] [INFO] Task started: HMMsearch
[2023-03-18 22:02:57,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b22256/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference/reference_markers.hmm OceanDNA-b22256/protein.faa > /dev/null
[2023-03-18 22:02:57,789] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:02:57,789] [INFO] Found 6/6 markers.
[2023-03-18 22:02:57,806] [INFO] Query marker FASTA was written to OceanDNA-b22256/markers.fasta
[2023-03-18 22:02:57,807] [INFO] Task started: Blastn
[2023-03-18 22:02:57,807] [INFO] Running command: blastn -query OceanDNA-b22256/markers.fasta -db /var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference/reference_markers.fasta -out OceanDNA-b22256/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:02:58,335] [INFO] Task succeeded: Blastn
[2023-03-18 22:02:58,336] [INFO] Selected 28 target genomes.
[2023-03-18 22:02:58,337] [INFO] Target genome list was writen to OceanDNA-b22256/target_genomes.txt
[2023-03-18 22:02:58,351] [INFO] Task started: fastANI
[2023-03-18 22:02:58,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg67f48c7e-8b57-4051-979d-72d6cd70765c/OceanDNA-b22256.fa --refList OceanDNA-b22256/target_genomes.txt --output OceanDNA-b22256/fastani_result.tsv --threads 1
[2023-03-18 22:03:20,708] [INFO] Task succeeded: fastANI
[2023-03-18 22:03:20,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:03:20,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:03:20,709] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:03:20,709] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:03:20,709] [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
--------------------------------------------------------------------------------
[2023-03-18 22:03:20,710] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22256/tc_result.tsv
[2023-03-18 22:03:20,710] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:03:20,710] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:03:20,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference/checkm_data
[2023-03-18 22:03:20,713] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:03:20,718] [INFO] Task started: CheckM
[2023-03-18 22:03:20,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22256/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22256/checkm_input OceanDNA-b22256/checkm_result
[2023-03-18 22:04:07,235] [INFO] Task succeeded: CheckM
[2023-03-18 22:04:07,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:04:07,240] [INFO] ===== Completeness check finished =====
[2023-03-18 22:04:07,240] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:04:07,240] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22256/markers.fasta)
[2023-03-18 22:04:07,241] [INFO] Task started: Blastn
[2023-03-18 22:04:07,241] [INFO] Running command: blastn -query OceanDNA-b22256/markers.fasta -db /var/lib/cwl/stgc0f17cd2-340f-4176-89b1-7fef0c197af3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22256/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:04:08,004] [INFO] Task succeeded: Blastn
[2023-03-18 22:04:08,006] [INFO] Selected 18 target genomes.
[2023-03-18 22:04:08,006] [INFO] Target genome list was writen to OceanDNA-b22256/target_genomes_gtdb.txt
[2023-03-18 22:04:08,043] [INFO] Task started: fastANI
[2023-03-18 22:04:08,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg67f48c7e-8b57-4051-979d-72d6cd70765c/OceanDNA-b22256.fa --refList OceanDNA-b22256/target_genomes_gtdb.txt --output OceanDNA-b22256/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:04:16,518] [INFO] Task succeeded: fastANI
[2023-03-18 22:04:16,526] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:04:16,526] [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_002709755.1	s__UBA8087 sp002709755	99.0257	742	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	98.89	98.89	0.90	0.90	2	conclusive
GCA_902521645.1	s__UBA8087 sp902521645	81.147	237	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684315.1	s__UBA8087 sp002684315	80.915	482	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862305.1	s__UBA8087 sp002862305	77.8077	199	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171655.1	s__UBA8087 sp002171655	77.1934	153	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	100.00	100.00	0.94	0.94	2	-
GCA_002684755.1	s__UBA12014 sp002684755	76.4033	69	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	76.2022	72	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891095.1	s__QWPT01 sp903891095	76.1669	54	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.40	98.92	0.94	0.91	5	-
GCA_016795065.1	s__JAEUIT01 sp016795065	76.1257	60	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__JAEUIT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883105.1	s__UBA966 sp018883105	76.0816	51	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684855.1	s__UBA12014 sp002684855	76.0401	68	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683195.1	s__GCA-002862325 sp002683195	75.9545	76	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167845.2	s__UBA12014 sp002167845	75.8463	73	806	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.48	99.48	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:04:16,527] [INFO] GTDB search result was written to OceanDNA-b22256/result_gtdb.tsv
[2023-03-18 22:04:16,528] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:04:16,529] [INFO] DFAST_QC result json was written to OceanDNA-b22256/dqc_result.json
[2023-03-18 22:04:16,529] [INFO] DFAST_QC completed!
[2023-03-18 22:04:16,529] [INFO] Total running time: 0h1m35s