[2023-03-15 14:29:06,009] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:29:06,010] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:29:06,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference
[2023-03-15 14:29:07,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:29:07,158] [INFO] Task started: Prodigal
[2023-03-15 14:29:07,158] [INFO] Running command: cat /var/lib/cwl/stg1fe9f740-3d1b-4b63-aebd-fe042e5a782c/OceanDNA-b15975.fa | prodigal -d OceanDNA-b15975/cds.fna -a OceanDNA-b15975/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:29:13,413] [INFO] Task succeeded: Prodigal
[2023-03-15 14:29:13,413] [INFO] Task started: HMMsearch
[2023-03-15 14:29:13,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b15975/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference/reference_markers.hmm OceanDNA-b15975/protein.faa > /dev/null
[2023-03-15 14:29:13,582] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:29:13,582] [INFO] Found 6/6 markers.
[2023-03-15 14:29:13,590] [INFO] Query marker FASTA was written to OceanDNA-b15975/markers.fasta
[2023-03-15 14:29:13,591] [INFO] Task started: Blastn
[2023-03-15 14:29:13,591] [INFO] Running command: blastn -query OceanDNA-b15975/markers.fasta -db /var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference/reference_markers.fasta -out OceanDNA-b15975/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:14,139] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:14,140] [INFO] Selected 15 target genomes.
[2023-03-15 14:29:14,140] [INFO] Target genome list was writen to OceanDNA-b15975/target_genomes.txt
[2023-03-15 14:29:14,149] [INFO] Task started: fastANI
[2023-03-15 14:29:14,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fe9f740-3d1b-4b63-aebd-fe042e5a782c/OceanDNA-b15975.fa --refList OceanDNA-b15975/target_genomes.txt --output OceanDNA-b15975/fastani_result.tsv --threads 1
[2023-03-15 14:29:25,206] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:25,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:29:25,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:29:25,207] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:29:25,207] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:29:25,207] [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 14:29:25,207] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15975/tc_result.tsv
[2023-03-15 14:29:25,207] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:29:25,207] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:29:25,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference/checkm_data
[2023-03-15 14:29:25,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:29:25,213] [INFO] Task started: CheckM
[2023-03-15 14:29:25,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15975/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15975/checkm_input OceanDNA-b15975/checkm_result
[2023-03-15 14:29:45,887] [INFO] Task succeeded: CheckM
[2023-03-15 14:29:45,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:29:45,889] [INFO] ===== Completeness check finished =====
[2023-03-15 14:29:45,889] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:29:45,890] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15975/markers.fasta)
[2023-03-15 14:29:45,890] [INFO] Task started: Blastn
[2023-03-15 14:29:45,890] [INFO] Running command: blastn -query OceanDNA-b15975/markers.fasta -db /var/lib/cwl/stg20799e24-f6b7-4690-94e6-9be3f17a5e27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15975/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:29:46,808] [INFO] Task succeeded: Blastn
[2023-03-15 14:29:46,809] [INFO] Selected 11 target genomes.
[2023-03-15 14:29:46,809] [INFO] Target genome list was writen to OceanDNA-b15975/target_genomes_gtdb.txt
[2023-03-15 14:29:46,824] [INFO] Task started: fastANI
[2023-03-15 14:29:46,825] [INFO] Running command: fastANI --query /var/lib/cwl/stg1fe9f740-3d1b-4b63-aebd-fe042e5a782c/OceanDNA-b15975.fa --refList OceanDNA-b15975/target_genomes_gtdb.txt --output OceanDNA-b15975/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:29:49,303] [INFO] Task succeeded: fastANI
[2023-03-15 14:29:49,309] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:29:49,310] [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_003476885.1	s__Limnocylindrus sp003476885	95.1873	205	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903937225.1	s__Limnocylindrus sp903937225	92.9801	198	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670475.1	s__Limnocylindrus sp003670475	82.5444	178	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.28	98.28	0.88	0.88	2	-
GCA_903944295.1	s__Limnocylindrus sp903944295	82.3624	173	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	99.38	99.18	0.85	0.81	11	-
GCA_903847005.1	s__Limnocylindrus sp903847005	81.3892	149	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670745.1	s__Limnocylindrus sp003670745	78.6313	106	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463555.1	s__Limnocylindrus sp016463555	78.5825	93	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.54	98.47	0.78	0.78	3	-
GCA_903820655.1	s__Limnocylindrus sp903820655	78.187	69	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864185.1	s__Limnocylindrus sp903864185	77.8876	85	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.90	97.48	0.92	0.89	6	-
GCA_903851225.1	s__Limnocylindrus sp903851225	77.4619	82	307	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	97.90	97.90	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-03-15 14:29:49,310] [INFO] GTDB search result was written to OceanDNA-b15975/result_gtdb.tsv
[2023-03-15 14:29:49,310] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:29:49,311] [INFO] DFAST_QC result json was written to OceanDNA-b15975/dqc_result.json
[2023-03-15 14:29:49,311] [INFO] DFAST_QC completed!
[2023-03-15 14:29:49,311] [INFO] Total running time: 0h0m43s