[2023-03-14 11:40:05,636] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,638] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference
[2023-03-14 11:40:06,729] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,730] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,730] [INFO] Running command: cat /var/lib/cwl/stgbd1b6a76-9d9f-4d15-9be3-5a0ca0e9627f/OceanDNA-a2581.fa | prodigal -d OceanDNA-a2581/cds.fna -a OceanDNA-a2581/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:18,696] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:18,696] [INFO] Task started: HMMsearch
[2023-03-14 11:40:18,696] [INFO] Running command: hmmsearch --tblout OceanDNA-a2581/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference/reference_markers.hmm OceanDNA-a2581/protein.faa > /dev/null
[2023-03-14 11:40:18,862] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:18,862] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbd1b6a76-9d9f-4d15-9be3-5a0ca0e9627f/OceanDNA-a2581.fa]
[2023-03-14 11:40:18,881] [INFO] Query marker FASTA was written to OceanDNA-a2581/markers.fasta
[2023-03-14 11:40:18,882] [INFO] Task started: Blastn
[2023-03-14 11:40:18,883] [INFO] Running command: blastn -query OceanDNA-a2581/markers.fasta -db /var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference/reference_markers.fasta -out OceanDNA-a2581/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:19,313] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:19,317] [INFO] Selected 5 target genomes.
[2023-03-14 11:40:19,317] [INFO] Target genome list was writen to OceanDNA-a2581/target_genomes.txt
[2023-03-14 11:40:19,320] [INFO] Task started: fastANI
[2023-03-14 11:40:19,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd1b6a76-9d9f-4d15-9be3-5a0ca0e9627f/OceanDNA-a2581.fa --refList OceanDNA-a2581/target_genomes.txt --output OceanDNA-a2581/fastani_result.tsv --threads 1
[2023-03-14 11:40:21,843] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:21,843] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:21,843] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:21,843] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:21,843] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:40:21,843] [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
--------------------------------------------------------------------------------
[2023-03-14 11:40:21,845] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2581/tc_result.tsv
[2023-03-14 11:40:21,848] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:21,848] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:21,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference/checkm_data
[2023-03-14 11:40:21,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:21,855] [INFO] Task started: CheckM
[2023-03-14 11:40:21,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2581/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2581/checkm_input OceanDNA-a2581/checkm_result
[2023-03-14 11:40:56,664] [INFO] Task succeeded: CheckM
[2023-03-14 11:40:56,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:40:56,679] [INFO] ===== Completeness check finished =====
[2023-03-14 11:40:56,679] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:40:56,679] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2581/markers.fasta)
[2023-03-14 11:40:56,680] [INFO] Task started: Blastn
[2023-03-14 11:40:56,680] [INFO] Running command: blastn -query OceanDNA-a2581/markers.fasta -db /var/lib/cwl/stg1689129a-3b98-4f32-bb53-c0834e111c13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2581/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:57,114] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:57,119] [INFO] Selected 12 target genomes.
[2023-03-14 11:40:57,119] [INFO] Target genome list was writen to OceanDNA-a2581/target_genomes_gtdb.txt
[2023-03-14 11:40:57,126] [INFO] Task started: fastANI
[2023-03-14 11:40:57,126] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd1b6a76-9d9f-4d15-9be3-5a0ca0e9627f/OceanDNA-a2581.fa --refList OceanDNA-a2581/target_genomes_gtdb.txt --output OceanDNA-a2581/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:01,175] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:01,182] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:41:01,182] [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_002506275.1	s__MGIIa-L1 sp002506275	99.7702	332	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	98.77	0.87	0.72	5	conclusive
GCA_018691345.1	s__MGIIa-L1 sp018691345	86.962	470	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018701175.1	s__MGIIa-L1 sp018701175	82.261	405	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.50	99.46	0.87	0.84	5	-
GCA_009937025.1	s__MGIIa-L1 sp009937025	78.3746	198	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182715.1	s__MGIIa-L1 sp905182715	78.2586	191	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687075.1	s__MGIIa-L1 sp002687075	78.2421	206	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	96.38	95.66	0.88	0.80	4	-
GCA_002499705.1	s__MGIIa-L1 sp002499705	78.2118	200	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182725.1	s__MGIIa-L1 sp905182725	77.9197	197	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018662825.1	s__MGIIa-L1 sp018662825	77.8771	197	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
GCA_002499545.1	s__MGIIa-L1 sp002499545	77.7004	149	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002495535.1	s__MGIIa-L1 sp002495535	77.004	106	617	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:01,183] [INFO] GTDB search result was written to OceanDNA-a2581/result_gtdb.tsv
[2023-03-14 11:41:01,187] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:01,190] [INFO] DFAST_QC result json was written to OceanDNA-a2581/dqc_result.json
[2023-03-14 11:41:01,190] [INFO] DFAST_QC completed!
[2023-03-14 11:41:01,190] [INFO] Total running time: 0h0m56s