[2023-06-13 07:44:42,232] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:44:42,234] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:44:42,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference
[2023-06-13 07:44:43,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:44:43,456] [INFO] Task started: Prodigal
[2023-06-13 07:44:43,456] [INFO] Running command: gunzip -c /var/lib/cwl/stgc01c2c82-24e0-4418-b39c-fb0ae66e4b52/GCA_022562215.1_ASM2256221v1_genomic.fna.gz | prodigal -d GCA_022562215.1_ASM2256221v1_genomic.fna/cds.fna -a GCA_022562215.1_ASM2256221v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:44:50,549] [INFO] Task succeeded: Prodigal
[2023-06-13 07:44:50,549] [INFO] Task started: HMMsearch
[2023-06-13 07:44:50,550] [INFO] Running command: hmmsearch --tblout GCA_022562215.1_ASM2256221v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference/reference_markers.hmm GCA_022562215.1_ASM2256221v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:44:50,776] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:44:50,777] [INFO] Found 6/6 markers.
[2023-06-13 07:44:50,806] [INFO] Query marker FASTA was written to GCA_022562215.1_ASM2256221v1_genomic.fna/markers.fasta
[2023-06-13 07:44:50,807] [INFO] Task started: Blastn
[2023-06-13 07:44:50,807] [INFO] Running command: blastn -query GCA_022562215.1_ASM2256221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference/reference_markers.fasta -out GCA_022562215.1_ASM2256221v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:44:51,490] [INFO] Task succeeded: Blastn
[2023-06-13 07:44:51,494] [INFO] Selected 20 target genomes.
[2023-06-13 07:44:51,495] [INFO] Target genome list was writen to GCA_022562215.1_ASM2256221v1_genomic.fna/target_genomes.txt
[2023-06-13 07:44:51,499] [INFO] Task started: fastANI
[2023-06-13 07:44:51,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgc01c2c82-24e0-4418-b39c-fb0ae66e4b52/GCA_022562215.1_ASM2256221v1_genomic.fna.gz --refList GCA_022562215.1_ASM2256221v1_genomic.fna/target_genomes.txt --output GCA_022562215.1_ASM2256221v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:45:06,962] [INFO] Task succeeded: fastANI
[2023-06-13 07:45:06,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:45:06,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:45:06,971] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 07:45:06,972] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 07:45:06,972] [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
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.9678	52	721	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	74.7613	63	721	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	74.7583	63	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 07:45:06,974] [INFO] DFAST Taxonomy check result was written to GCA_022562215.1_ASM2256221v1_genomic.fna/tc_result.tsv
[2023-06-13 07:45:06,974] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:45:06,975] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:45:06,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference/checkm_data
[2023-06-13 07:45:06,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:45:07,013] [INFO] Task started: CheckM
[2023-06-13 07:45:07,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022562215.1_ASM2256221v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022562215.1_ASM2256221v1_genomic.fna/checkm_input GCA_022562215.1_ASM2256221v1_genomic.fna/checkm_result
[2023-06-13 07:45:33,070] [INFO] Task succeeded: CheckM
[2023-06-13 07:45:33,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 07:45:33,093] [INFO] ===== Completeness check finished =====
[2023-06-13 07:45:33,093] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:45:33,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022562215.1_ASM2256221v1_genomic.fna/markers.fasta)
[2023-06-13 07:45:33,094] [INFO] Task started: Blastn
[2023-06-13 07:45:33,094] [INFO] Running command: blastn -query GCA_022562215.1_ASM2256221v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b49e0a0-d26e-42d5-af77-e5240bc763fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_022562215.1_ASM2256221v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:45:34,163] [INFO] Task succeeded: Blastn
[2023-06-13 07:45:34,167] [INFO] Selected 13 target genomes.
[2023-06-13 07:45:34,168] [INFO] Target genome list was writen to GCA_022562215.1_ASM2256221v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:45:34,174] [INFO] Task started: fastANI
[2023-06-13 07:45:34,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgc01c2c82-24e0-4418-b39c-fb0ae66e4b52/GCA_022562215.1_ASM2256221v1_genomic.fna.gz --refList GCA_022562215.1_ASM2256221v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022562215.1_ASM2256221v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:45:43,099] [INFO] Task succeeded: fastANI
[2023-06-13 07:45:43,120] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 07:45:43,120] [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_004356735.1	s__SMWR01 sp004356735	94.1554	412	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__SMWR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.9918	107	721	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_002729515.1	s__GCA-2729515 sp002729515	76.9192	121	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215615.1	s__JABSQX01 sp013215615	76.5787	88	721	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_002687015.1	s__GCA-2687015 sp002687015	76.1713	117	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875225.1	s__VGRW01 sp016875225	76.1276	70	721	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_018262315.1	s__PR03 sp018262315	76.1194	64	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.0074	119	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.9343	100	721	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_016875395.1	s__VGRF01 sp016875395	75.9025	106	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051925.1	s__UBA4427 sp011051925	75.4597	53	721	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 07:45:43,122] [INFO] GTDB search result was written to GCA_022562215.1_ASM2256221v1_genomic.fna/result_gtdb.tsv
[2023-06-13 07:45:43,123] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:45:43,126] [INFO] DFAST_QC result json was written to GCA_022562215.1_ASM2256221v1_genomic.fna/dqc_result.json
[2023-06-13 07:45:43,126] [INFO] DFAST_QC completed!
[2023-06-13 07:45:43,126] [INFO] Total running time: 0h1m1s