[2023-03-15 15:18:22,063] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,065] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,065] [INFO] DQC Reference Directory: /var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference
[2023-03-15 15:18:23,232] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,232] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,232] [INFO] Running command: cat /var/lib/cwl/stgcc5f020f-c188-404f-9377-0d7caa207330/OceanDNA-b2444.fa | prodigal -d OceanDNA-b2444/cds.fna -a OceanDNA-b2444/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:26,463] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:26,463] [INFO] Task started: HMMsearch
[2023-03-15 15:18:26,463] [INFO] Running command: hmmsearch --tblout OceanDNA-b2444/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference/reference_markers.hmm OceanDNA-b2444/protein.faa > /dev/null
[2023-03-15 15:18:26,619] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:26,619] [INFO] Found 6/6 markers.
[2023-03-15 15:18:26,629] [INFO] Query marker FASTA was written to OceanDNA-b2444/markers.fasta
[2023-03-15 15:18:26,629] [INFO] Task started: Blastn
[2023-03-15 15:18:26,629] [INFO] Running command: blastn -query OceanDNA-b2444/markers.fasta -db /var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference/reference_markers.fasta -out OceanDNA-b2444/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:27,148] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:27,150] [INFO] Selected 21 target genomes.
[2023-03-15 15:18:27,151] [INFO] Target genome list was writen to OceanDNA-b2444/target_genomes.txt
[2023-03-15 15:18:27,166] [INFO] Task started: fastANI
[2023-03-15 15:18:27,166] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc5f020f-c188-404f-9377-0d7caa207330/OceanDNA-b2444.fa --refList OceanDNA-b2444/target_genomes.txt --output OceanDNA-b2444/fastani_result.tsv --threads 1
[2023-03-15 15:18:35,258] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:35,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:35,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:35,259] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:18:35,259] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:18:35,259] [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
--------------------------------------------------------------------------------
[2023-03-15 15:18:35,262] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2444/tc_result.tsv
[2023-03-15 15:18:35,265] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:35,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:35,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference/checkm_data
[2023-03-15 15:18:35,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:35,307] [INFO] Task started: CheckM
[2023-03-15 15:18:35,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2444/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2444/checkm_input OceanDNA-b2444/checkm_result
[2023-03-15 15:18:49,941] [INFO] Task succeeded: CheckM
[2023-03-15 15:18:49,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:18:49,948] [INFO] ===== Completeness check finished =====
[2023-03-15 15:18:49,949] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:18:49,949] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2444/markers.fasta)
[2023-03-15 15:18:49,950] [INFO] Task started: Blastn
[2023-03-15 15:18:49,950] [INFO] Running command: blastn -query OceanDNA-b2444/markers.fasta -db /var/lib/cwl/stgc66c91f2-37f6-47a6-b458-01d2533b038e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2444/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:50,673] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:50,679] [INFO] Selected 7 target genomes.
[2023-03-15 15:18:50,679] [INFO] Target genome list was writen to OceanDNA-b2444/target_genomes_gtdb.txt
[2023-03-15 15:18:50,688] [INFO] Task started: fastANI
[2023-03-15 15:18:50,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc5f020f-c188-404f-9377-0d7caa207330/OceanDNA-b2444.fa --refList OceanDNA-b2444/target_genomes_gtdb.txt --output OceanDNA-b2444/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:18:51,990] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:51,995] [INFO] Found 7 fastANI hits (4 hits with ANI > circumscription radius)
[2023-03-15 15:18:51,995] [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_003213625.1	s__Actinomarina sp003213625	96.8653	190	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.18	95.09	0.86	0.82	29	inconclusive
GCA_000384495.1	s__Actinomarina sp000384495	95.9072	110	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.56	95.50	0.68	0.67	3	inconclusive
GCA_902587025.1	s__Actinomarina sp902587025	95.6364	154	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.69	95.12	0.65	0.61	5	inconclusive
GCA_902619825.1	s__Actinomarina sp902619825	95.4281	196	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.86	0.86	2	inconclusive
GCA_902615855.1	s__Actinomarina sp902615855	94.72	186	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526825.1	s__Actinomarina sp902526825	93.8515	152	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627635.1	s__Actinomarina sp902627635	92.9011	145	207	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:18:51,997] [INFO] GTDB search result was written to OceanDNA-b2444/result_gtdb.tsv
[2023-03-15 15:18:51,998] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:18:52,000] [INFO] DFAST_QC result json was written to OceanDNA-b2444/dqc_result.json
[2023-03-15 15:18:52,000] [INFO] DFAST_QC completed!
[2023-03-15 15:18:52,000] [INFO] Total running time: 0h0m30s