[2023-06-28 02:21:49,534] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:21:49,539] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:21:49,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference
[2023-06-28 02:21:51,093] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:21:51,094] [INFO] Task started: Prodigal
[2023-06-28 02:21:51,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg71384317-be3d-4724-8f26-9d7b5010525e/GCA_019310405.1_ASM1931040v1_genomic.fna.gz | prodigal -d GCA_019310405.1_ASM1931040v1_genomic.fna/cds.fna -a GCA_019310405.1_ASM1931040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:22:04,358] [INFO] Task succeeded: Prodigal
[2023-06-28 02:22:04,359] [INFO] Task started: HMMsearch
[2023-06-28 02:22:04,359] [INFO] Running command: hmmsearch --tblout GCA_019310405.1_ASM1931040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference/reference_markers.hmm GCA_019310405.1_ASM1931040v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:22:04,666] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:22:04,667] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg71384317-be3d-4724-8f26-9d7b5010525e/GCA_019310405.1_ASM1931040v1_genomic.fna.gz]
[2023-06-28 02:22:04,718] [INFO] Query marker FASTA was written to GCA_019310405.1_ASM1931040v1_genomic.fna/markers.fasta
[2023-06-28 02:22:04,719] [INFO] Task started: Blastn
[2023-06-28 02:22:04,719] [INFO] Running command: blastn -query GCA_019310405.1_ASM1931040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference/reference_markers.fasta -out GCA_019310405.1_ASM1931040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:05,254] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:05,258] [INFO] Selected 20 target genomes.
[2023-06-28 02:22:05,259] [INFO] Target genome list was writen to GCA_019310405.1_ASM1931040v1_genomic.fna/target_genomes.txt
[2023-06-28 02:22:05,269] [INFO] Task started: fastANI
[2023-06-28 02:22:05,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg71384317-be3d-4724-8f26-9d7b5010525e/GCA_019310405.1_ASM1931040v1_genomic.fna.gz --refList GCA_019310405.1_ASM1931040v1_genomic.fna/target_genomes.txt --output GCA_019310405.1_ASM1931040v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:27,504] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:27,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:27,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:27,510] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:27,511] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:22:27,511] [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
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.8333	50	1249	95	below_threshold
Phytohabitans suffuscus	strain=NBRC 105367	GCA_011764565.1	624315	624315	type	True	74.6628	52	1249	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:22:27,514] [INFO] DFAST Taxonomy check result was written to GCA_019310405.1_ASM1931040v1_genomic.fna/tc_result.tsv
[2023-06-28 02:22:27,514] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:27,514] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:27,515] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference/checkm_data
[2023-06-28 02:22:27,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:27,571] [INFO] Task started: CheckM
[2023-06-28 02:22:27,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310405.1_ASM1931040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310405.1_ASM1931040v1_genomic.fna/checkm_input GCA_019310405.1_ASM1931040v1_genomic.fna/checkm_result
[2023-06-28 02:23:07,467] [INFO] Task succeeded: CheckM
[2023-06-28 02:23:07,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:23:07,491] [INFO] ===== Completeness check finished =====
[2023-06-28 02:23:07,492] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:23:07,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310405.1_ASM1931040v1_genomic.fna/markers.fasta)
[2023-06-28 02:23:07,492] [INFO] Task started: Blastn
[2023-06-28 02:23:07,493] [INFO] Running command: blastn -query GCA_019310405.1_ASM1931040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83885878-6cbc-428c-93b0-b31cf52e54a0/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310405.1_ASM1931040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:23:08,074] [INFO] Task succeeded: Blastn
[2023-06-28 02:23:08,078] [INFO] Selected 16 target genomes.
[2023-06-28 02:23:08,078] [INFO] Target genome list was writen to GCA_019310405.1_ASM1931040v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:23:08,112] [INFO] Task started: fastANI
[2023-06-28 02:23:08,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg71384317-be3d-4724-8f26-9d7b5010525e/GCA_019310405.1_ASM1931040v1_genomic.fna.gz --refList GCA_019310405.1_ASM1931040v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310405.1_ASM1931040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:23:22,417] [INFO] Task succeeded: fastANI
[2023-06-28 02:23:22,430] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:23:22,430] [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_012960035.1	s__DUBZ01 sp012960035	77.0608	199	1249	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__DUBZ01	95.0	99.83	99.83	0.93	0.93	2	-
GCA_016875225.1	s__VGRW01 sp016875225	75.7107	57	1249	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.6736	109	1249	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_013215615.1	s__JABSQX01 sp013215615	75.4816	71	1249	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_002709835.1	s__UBA4427 sp002709835	75.4582	53	1249	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_013215605.1	s__JABSQW01 sp013215605	75.4332	87	1249	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_014240165.1	s__JAZXM01 sp014240165	75.4109	56	1249	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JAZXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719955.1	s__UBA4427 sp002719955	75.3949	59	1249	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_016707895.1	s__UBA2376 sp016707895	74.884	59	1249	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	99.64	99.63	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-28 02:23:22,432] [INFO] GTDB search result was written to GCA_019310405.1_ASM1931040v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:23:22,433] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:23:22,435] [INFO] DFAST_QC result json was written to GCA_019310405.1_ASM1931040v1_genomic.fna/dqc_result.json
[2023-06-28 02:23:22,436] [INFO] DFAST_QC completed!
[2023-06-28 02:23:22,436] [INFO] Total running time: 0h1m33s