[2023-03-14 13:05:54,255] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:05:54,256] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:05:54,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference
[2023-03-14 13:05:55,327] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:05:55,328] [INFO] Task started: Prodigal
[2023-03-14 13:05:55,328] [INFO] Running command: cat /var/lib/cwl/stgc577e5aa-1f32-4bee-bc9c-9323d4960de0/OceanDNA-a2145.fa | prodigal -d OceanDNA-a2145/cds.fna -a OceanDNA-a2145/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:06:04,339] [INFO] Task succeeded: Prodigal
[2023-03-14 13:06:04,340] [INFO] Task started: HMMsearch
[2023-03-14 13:06:04,340] [INFO] Running command: hmmsearch --tblout OceanDNA-a2145/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference/reference_markers.hmm OceanDNA-a2145/protein.faa > /dev/null
[2023-03-14 13:06:04,504] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:06:04,504] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc577e5aa-1f32-4bee-bc9c-9323d4960de0/OceanDNA-a2145.fa]
[2023-03-14 13:06:04,516] [INFO] Query marker FASTA was written to OceanDNA-a2145/markers.fasta
[2023-03-14 13:06:04,518] [INFO] Task started: Blastn
[2023-03-14 13:06:04,518] [INFO] Running command: blastn -query OceanDNA-a2145/markers.fasta -db /var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference/reference_markers.fasta -out OceanDNA-a2145/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:06:04,942] [INFO] Task succeeded: Blastn
[2023-03-14 13:06:04,942] [INFO] Selected 7 target genomes.
[2023-03-14 13:06:04,943] [INFO] Target genome list was writen to OceanDNA-a2145/target_genomes.txt
[2023-03-14 13:06:04,946] [INFO] Task started: fastANI
[2023-03-14 13:06:04,947] [INFO] Running command: fastANI --query /var/lib/cwl/stgc577e5aa-1f32-4bee-bc9c-9323d4960de0/OceanDNA-a2145.fa --refList OceanDNA-a2145/target_genomes.txt --output OceanDNA-a2145/fastani_result.tsv --threads 1
[2023-03-14 13:06:07,341] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:07,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:06:07,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:06:07,342] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:06:07,342] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:06:07,342] [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 13:06:07,342] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2145/tc_result.tsv
[2023-03-14 13:06:07,342] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:06:07,342] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:06:07,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference/checkm_data
[2023-03-14 13:06:07,345] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:06:07,348] [INFO] Task started: CheckM
[2023-03-14 13:06:07,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2145/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2145/checkm_input OceanDNA-a2145/checkm_result
[2023-03-14 13:06:39,330] [INFO] Task succeeded: CheckM
[2023-03-14 13:06:39,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:06:39,332] [INFO] ===== Completeness check finished =====
[2023-03-14 13:06:39,332] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:06:39,333] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2145/markers.fasta)
[2023-03-14 13:06:39,334] [INFO] Task started: Blastn
[2023-03-14 13:06:39,334] [INFO] Running command: blastn -query OceanDNA-a2145/markers.fasta -db /var/lib/cwl/stg8279ca90-29bb-49aa-bd2b-468ec0e216c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2145/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:06:39,775] [INFO] Task succeeded: Blastn
[2023-03-14 13:06:39,776] [INFO] Selected 10 target genomes.
[2023-03-14 13:06:39,776] [INFO] Target genome list was writen to OceanDNA-a2145/target_genomes_gtdb.txt
[2023-03-14 13:06:39,813] [INFO] Task started: fastANI
[2023-03-14 13:06:39,814] [INFO] Running command: fastANI --query /var/lib/cwl/stgc577e5aa-1f32-4bee-bc9c-9323d4960de0/OceanDNA-a2145.fa --refList OceanDNA-a2145/target_genomes_gtdb.txt --output OceanDNA-a2145/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:06:43,617] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:43,621] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:06:43,621] [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_002506025.1	s__MGIIa-L1 sp002506025	93.2872	328	527	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_013329295.1	s__MGIIa-L1 sp9596u	78.4659	127	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
GCA_002496955.1	s__MGIIa-L1 sp002496955	78.1379	120	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.33	98.29	0.73	0.72	3	-
GCA_002688825.1	s__MGIIa-L1 sp002688825	76.9444	81	527	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_018667575.1	s__MGIIa-L1 sp018667575	76.2543	52	527	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.28	99.11	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-14 13:06:43,622] [INFO] GTDB search result was written to OceanDNA-a2145/result_gtdb.tsv
[2023-03-14 13:06:43,622] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:06:43,623] [INFO] DFAST_QC result json was written to OceanDNA-a2145/dqc_result.json
[2023-03-14 13:06:43,623] [INFO] DFAST_QC completed!
[2023-03-14 13:06:43,623] [INFO] Total running time: 0h0m49s