[2023-03-15 23:07:02,647] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:07:02,647] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:07:02,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference
[2023-03-15 23:07:03,966] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:07:03,966] [INFO] Task started: Prodigal
[2023-03-15 23:07:03,966] [INFO] Running command: cat /var/lib/cwl/stgbe922447-8b1f-441f-aa6e-527c93e2d90c/OceanDNA-b21014.fa | prodigal -d OceanDNA-b21014/cds.fna -a OceanDNA-b21014/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:07:18,984] [INFO] Task succeeded: Prodigal
[2023-03-15 23:07:18,984] [INFO] Task started: HMMsearch
[2023-03-15 23:07:18,984] [INFO] Running command: hmmsearch --tblout OceanDNA-b21014/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference/reference_markers.hmm OceanDNA-b21014/protein.faa > /dev/null
[2023-03-15 23:07:19,176] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:07:19,176] [INFO] Found 6/6 markers.
[2023-03-15 23:07:19,199] [INFO] Query marker FASTA was written to OceanDNA-b21014/markers.fasta
[2023-03-15 23:07:19,200] [INFO] Task started: Blastn
[2023-03-15 23:07:19,200] [INFO] Running command: blastn -query OceanDNA-b21014/markers.fasta -db /var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference/reference_markers.fasta -out OceanDNA-b21014/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:07:19,845] [INFO] Task succeeded: Blastn
[2023-03-15 23:07:19,846] [INFO] Selected 30 target genomes.
[2023-03-15 23:07:19,846] [INFO] Target genome list was writen to OceanDNA-b21014/target_genomes.txt
[2023-03-15 23:07:19,916] [INFO] Task started: fastANI
[2023-03-15 23:07:19,917] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe922447-8b1f-441f-aa6e-527c93e2d90c/OceanDNA-b21014.fa --refList OceanDNA-b21014/target_genomes.txt --output OceanDNA-b21014/fastani_result.tsv --threads 1
[2023-03-15 23:07:41,245] [INFO] Task succeeded: fastANI
[2023-03-15 23:07:41,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:07:41,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:07:41,249] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:07:41,249] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:07:41,249] [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
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.0755	55	792	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:07:41,250] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21014/tc_result.tsv
[2023-03-15 23:07:41,250] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:07:41,250] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:07:41,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference/checkm_data
[2023-03-15 23:07:41,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:07:41,255] [INFO] Task started: CheckM
[2023-03-15 23:07:41,255] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21014/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21014/checkm_input OceanDNA-b21014/checkm_result
[2023-03-15 23:08:20,259] [INFO] Task succeeded: CheckM
[2023-03-15 23:08:20,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.81%
Contamintation: 5.01%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 23:08:20,398] [INFO] ===== Completeness check finished =====
[2023-03-15 23:08:20,398] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:08:20,399] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21014/markers.fasta)
[2023-03-15 23:08:20,400] [INFO] Task started: Blastn
[2023-03-15 23:08:20,400] [INFO] Running command: blastn -query OceanDNA-b21014/markers.fasta -db /var/lib/cwl/stg8054213b-dd0d-4ab2-91c1-d53521af42d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21014/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:08:21,522] [INFO] Task succeeded: Blastn
[2023-03-15 23:08:21,544] [INFO] Selected 27 target genomes.
[2023-03-15 23:08:21,544] [INFO] Target genome list was writen to OceanDNA-b21014/target_genomes_gtdb.txt
[2023-03-15 23:08:21,586] [INFO] Task started: fastANI
[2023-03-15 23:08:21,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe922447-8b1f-441f-aa6e-527c93e2d90c/OceanDNA-b21014.fa --refList OceanDNA-b21014/target_genomes_gtdb.txt --output OceanDNA-b21014/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:08:39,431] [INFO] Task succeeded: fastANI
[2023-03-15 23:08:39,438] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:08:39,438] [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_013215615.1	s__JABSQX01 sp013215615	77.0064	100	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.651	158	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.551	162	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	76.2336	117	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.2334	131	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051925.1	s__UBA4427 sp011051925	76.2177	85	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687015.1	s__GCA-2687015 sp002687015	76.1782	125	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	76.081	74	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	75.857	147	792	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005879585.1	s__DP-3 sp005879585	75.3663	53	792	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888095.1	s__DP-3 sp005888095	75.157	60	792	d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UTPRO1;f__DP-6;g__DP-3	95.0	98.46	98.46	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-15 23:08:39,440] [INFO] GTDB search result was written to OceanDNA-b21014/result_gtdb.tsv
[2023-03-15 23:08:39,440] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:08:39,443] [INFO] DFAST_QC result json was written to OceanDNA-b21014/dqc_result.json
[2023-03-15 23:08:39,444] [INFO] DFAST_QC completed!
[2023-03-15 23:08:39,444] [INFO] Total running time: 0h1m37s